The 2.0 engines and bellhousings (both manual and auto) use hollow locating dowels that measure about 0.5" in diameter. The 2.3 engines and bellhousings (both manual and auto) use hollow locating dowels that measure about 0.6" in diameter. So when using a 2.0 bellhousing on a 2.3 engine, a stepped hollow locating dowel can be used to allow it sit flush and aligned. As an alternative, the 2.0 bellhousing locating dowel hole could be bored out to the 2.3's larger size but the machining needs to be precise for alignment.
On the two sets of 2.3 block upper mounting holes, I suspect we are not thinking of the same thing. To rephrase, the early 2.3 blocks (70's & 80's) have 8 holes drilled and tapped for bolting down the bellhousings but only six of the holes are used. The extra 2 holes are at the top of the block, see photos. The early auto bellhousings use the lower of the 2 upper holes. The late autos (~90's) and manuals ( early and late) use the upper of the 2 upper mounting holes. This is the same for both NA and turbo blocks. The above is based on the parts that I have. I have the following early 2.3 blocks that have the two sets of upper holes (8 total holes): 79NA, 86T, 87T, 88T, and 89NA. I have the following late 2.3 blocks with just the upper of the two set of upper holes (6 total holes): 93NA, 95NA, and 98NA. Hope this did not confuse it further.
On a side note, the 2.0 bellhousings (both auto and manual) would use the lower of the two sets of upper holes on the 2.3 blocks.