this thread is OLD AF but its one of the first hits that come up for differences between the blocks. I have multiples of each in my possession and have done a lot of 24v builds including hybrid builds... how here is a brain dump for the community... this is backed with hands-on-parts experience so if you disagree with some points, then you're probably wrong, sorry.
... in no particular order at all, and excluding FSI R32 in all cases:
1. blocks are same casting. touareg and other SUV 3.2's have the bosses for transverse mounting points on passenger side, but the holes are not drilled or tapped. it is 100% safe to do this yourself, just line it up carefully.
2. crankshafts are the same. actually side bar, but a 12v and a 24v (2.8) have same part number crankshaft, just different timing wheel. the 3.2 is obviously a larger crankshaft but with same wheel as 2.8 24v.
3. all vr6 engines use same main bearings and main bolts/studs.
4. all 12v/24v/r32 use same oil pump up to 2006 (and can exchange different pans) except the SUV's and phaetons which use a very deep pump to match their deep pans. Phaetons have less deep pans and fit audi longitudinal A4/S4 swaps perfectly without modifying and use a slightly different oil pump again. these are liquid diamond flavoured gold if you ever find one... sell it and buy a house with the proceeds, lol.
5. all VR6 blocks have the 'legacy mounts" which were originally mk3 rear block mounts, and are no longer legacy, as all modern VR6's in longitudinal applications are using these again... will be great for R44 future swaps into mk2's lol.
6. cams in all non-FSI R32 engines are the same... actually they are the same part numbers as 24v (BDF) and equivalent blocks too... no difference, sorry.
7. cylinder heads for all non-FSI R32 engines are 100% identical (at least in north america and my experience). fun fact... the intake flange on 3.2 is vertical... 2.8 has an angled inlet and is the real reason you cannot swap 2.8-3.2 intake manifolds... would either be an interference fit or put it up through the hood depending on what's swapping onto what... the flange itself is compatible for things like short runner intakes, but be aware that it will tilt up and closer to the head on a 24v 2.8... some fuel rails won't work like this.
8. knock sensors and crank position sensors on all 24v engines are the same.
9. valve covers on 2.8 and 3.2 (non-FSI) are all interchangeble, but have different brackets hanging off of them depending what they came on.
10. exhaust flanges for 2.8 and 3.2 are the same, but the 3.2 has 2x studs in a slightly different place. you can just drill for the difference in a swap... don't believe me? say i'm a liar haha... well the mk4 R32 and the 24v 2.8's share identical exhaust manifold part numbers, but the limited production R32 ones were modified and part number not changed... many aftermarket turbo exhaust manifolds are drilled for both. same goes for gaskets.
11. R32 uses smaller bodied spark plugs and ignition coils than almost every other modern water-cooled vw/audi. You need a smaller bodied spark plug removal tool, and 24v BDF coilpacks won't fit down into the holes.
12. mind blower.... ALL non-FSI vr6 connection rods are the same part number right back from AAA 12v up to BJS/BUB engines. same bearings, same rods. part numbers matching.
13. R32 has same coolant flange on head as touareg, except the small seperate nozzle to flow to bottom of rad is made as a mirror image for touareg as its hose runs along hte exhaust side of the engine to reach passenger side of SUV... in a pinch, you can still use it, just redrill holes (sketchy but would get a person home in a bind).
14. all non-FSI VR6 blocks use same lower timing chains, tension, guides right up to the intermediate shaft oil pump drive. rarely fail except where poor oiling is concerned.
15. the accessory bracket is very different between R32 and SUV 24v's... 100% incompatible between platform, but you can mount any type you want onto any 24v block. Ex: i have a touareg R32 with a mk4 bracket, and am building up a 2.8L with touareg bracket and accessories for a B6 S4 longitudinal swap lol.
16. ALL VR6 engines have identical crankshaft mounting face so any flywheel can go on any vr6....
17. NOT ALL vr6 engines have identical transmission mounting face... even within vr golf/jetta family there is a difference... automatic 24v engines 'sometimes' have one of the alignment pegs in a completely different and incompatible location outside of the 02m/02j/02a mounting area. can fix by removing the alignment peg... not ideal. i have never seen a touareg 3.2 that didn't match a FWD trans bellhousing which is good.
18. super-vr6-nerds will know that a mk5 R32 has a shallower oil pump and can be used to get extra clearance in a mk4/mk3/mk2 with a short pan. you can buy such a contraption for about $700 USD or buy a new mk3 steel pan, chop the bottom and weld is shorter.
19. R32 engines have a really really large oil cooler compared to 2.8L engines and will interchange for extra oil cooling on BDF turbo engines.
20. throttle bodies in mk4 R32 have coolant tempering lines, the SUV's do not. not sure on phaeton or passats.
21. VR5 (10v and 20v versions) in europe had an adapter plate between them and the transmissions in B4/b5 passats that were still longitudinal... this will bolt to every audi car chassis transmission there is in last 25 years+.... longitudinal swaps

works on any vr6 with noted provision in #17 above.
22. vr5 driver's side (left) mount is a perfect fit for an audi a4/s4 longitudinal swap and has integrated oil cooler. the passenger side (right) is not as the vr6's lack special mounts the shorter vr5 has between oil pump drive boss and flywheel end... but its easy to manufacture at home.
23. R32 and touareg engines all have the same pistons, rings, valves, etc.
24. R32 and touareg engines have identical timing chain parts... zero difference between them. i have never confirmed if the camshaft timing wheels differ but will later today. 2.8 and 3.2 R32 are the same... never checked touareg in particular.
25. touareg 3.2's have plastic front main seal and some rear main seal flanges... form-fit-function identical, just different material of construction. this matches many newer VW/audi engines.
26. timing covers for 3.2 engines all fit between each other but some external features vary. i am not aware of any clearance issues with FWD transmissions but haven't confirmed all combos... i do know 12v covers need trimming to go on many audi transmissions.
27. valve covers vary in layout with a few different versions... mk4 R32 has low chain cover, pulley side PCV vent, chain side oil fill cap. touareg has high chain cover pulley side oil fill cap chain side PCV, mk5 r32/TTr32 has high chain cover, chain side fill and PCV (perfect for audi long swaps). all are interchangeable, some have benefits for certain swaps/hybrid builds.
28. 2.8 and mk4 have PCV on pulley end which needs long plastic PCV hoses which break with age. the touareg intake manifold has a short tiny little hose from chain side of valve cover right to backside of throttle body area. is cleaner and also doesn't fill up cyl 1, 2,3 with grime so much. many 24v 2.8 and 3.2 suffer from low compression on cyl 1-3 due to valve lip grime build-up.
29. touareg fuel rails are non-return rails (ie - only 1 supply line to it). mk4 R32 needs return loop rail, mk5 R32 does not.
29. touareg serpentine belt and crank pulley have 7-ribs... R32 has 6-ribs.
most of this is useless, but i am sure some of it will satisfy decision to use low-cost touareg 3.2's for transverse swaps
oh... yes, you absolutely can use a touareg 3.2 to swap into a golf/jetta. here is what you need to do:
1. tap 3x mounting holes into the bosses on the block.
2. swap oil pump and pan from R32 or 2.8 24v onto the touareg block
3. swap R32/24v exhaust manifolds (they point down, touareg points to side a bit) no change for a mk5 R32 to touareg
4. swap accessory bracket and accessories
5. swap R32 fuel rail onto touareg head
6. swap intake mani and valve cover if you want to keep same connections in the car as R32/24v/TT
7. swap coolant flange over thermostat
8. swap oil cooler assembly and hoses between block and cooler
9. swap crank pulley if you are bothered the touareg ones have 7-ribs...