It's possible that the mech board isn't good for you, though, as others have replied, o-rings are definitely worth a shot: they soften the landing as well as reduce noise. I've put o-rings on every board with Cherry switches I've owned (though only on the alpha and punctuation keys; I don't see a need on the other keys). O-rings are cheap and very easy to install. I have a board with o-ringed browns, and it's very comfortable, but it's also possible that a board with higher actuation force would be better because you wouldn't slam as hard at bottom. You might also like a Topre board because they feel somewhat like rubber domes, but they're pricey.
I don't know if anyone really knows the answer to your first two questions. I mostly bottom out, at least in part because I learned to type roughly 60 years ago on manual typewriters when keyboards were really mechanical, and there was no such thing as not bottoming out. The good news is that in the years since, I've done a lot of typing (I'm a writer), with a lot of bottoming out, and my fingers are doing just fine.
The whole keyboard thing is very subjective. You see lots of strong opinions on this board, but the only right keyboard for you is the one that feels good and works for you. For some people, that's a rubber dome.