a) trees and rocks are part of the world and removal has to be saved, yes.

b) no, the terrain will never be exactly the same in terms of bits and bytes down in the file. It has to save the modification.

c) the main issue is just load times. I have a similar setup, a single world where I bashed around for months. It is hundreds of MB and takes 5 seconds or so to save now on SSD on a high end machine. On my old box before, it took 30+ seconds (but that was pre H&H if there has been any file performance optimizations). I am not aware of any crashing or other fails due to large file size; as I understand the game it loads 'areas' that are 'around' the active player for sure, but what I do not understand is how it handles areas you are not in (eg, your farm back home grows etc). When I portal to my remote plains farm to harvest, though, the plants load in immature, then a small time passes (2-3 seconds) and they all mature and are ready to harvest. So that makes me think that are was not loaded and when it was pulled in from me visiting, it updated the timers at that point. Same for fueled fires etc?
Anyway, your biggest performance hit from my understand of it is massive terraforms to a single area (eg, large homes or playing dig-dug) and the hits when the world save comes.