Engine removal/swap question

[JeepOfTheseus]

So I know the hemi swaps just lift the body and do the swap with the chassis fully exposed. I'm sure that makes it a lot easier, but is that also done because it's required to remove even just the stock engine? I'm having mine replaced, which doesn't include a new transmission...and after doing a little inspecting it got me wondering - how do you remove the two nuts on top of the transmission housing with it in place? In fact, they seem like bolts/studs that go into the block, so how would you even cherry pick it out?

I have a lot of wiring that is going to make lifting the body problematic, so just trying to get ahead of this.

edit: I guess the other option is...do they remove it with the transmission intact and then just swap it over?

Sponsored