Just sharing my experience: some friends of mine of myself took the Buquebus boat service from Buenos Aires to Montevideo, then back from Montevideo to Buenos Aires on the same day in early January 2020.
None of us received an Uruguayan stamp on their passport upon passing the Uruguayan immigration (we went through 2 Uruguayan immigration officers) at the ...
The entire Subte network (sans the Premetro Light Rail and Urquiza Line + various train yards) is underground, so there are no major elevated portions of the network.
If you are visiting to see elevated stations, I believe some of the commuter rail lines just underwent considerable grade separation projects, but those are technically not part of the Subte.
I don't think so. This terminal is indeed structured like an airport, with check-in and stuff, but there is fewer hassles - not that much of security theatre, boarding is faster, boats don't need time to steer around like planes do, etc. I think 45 minutes is more than enough to board the ship, I don't think they are leaving without you.
Having done this a couple times I can say that your passport will be stamped twice: once for entry and once for exit. In general, the two immigration checks - Argentinian and Uruguayan - are back to back so the likelihood of missing out on a stamp is fairly low.