It is the top die that is very thin. Which is the height that the bottom die would need to be reduced by, in order to maintain the same height.
For SoIC, hybrid bond, there would not be any micro-bumps. As far as we know, AMD is not planning on using micro-bumps for stacking, mainly because SoIC hybrid bond is a generation ahead of it.
As far as TSV depth, I am not sure from which side they are counting. If it is 10-200 um from the top die, it means that TSMC would be shooting for 10um end so that more than enough of the TSV is exposed by polishing off the 50 um from the top.
But TSMC / AMD don't necessarily have to shoot for the thinnest die, since on Zen 3, we may not necessarily see more than 1 level.
It seems that going from 0 to 1 layer is hard, going from 1 to 2 is hard, but then going from 2 to more layers would just re-use the same technique that was used in going from 1 to 2.
Edit: I was wrong. In this AMD video, they show that it is the core die that is shaved to the thinnest height, they said 20 um:
So we know that AMD tackled the 0 to 1 layer, but we don't know if the > 1 layer has been tackled...