They could have done the tree thing, it isn't an especially process intensive thing to do with a single tree (entire forests would be a different matter altogether), the reason it didn't happen was it wasn't really in the plans and it was a silly idea that Molyneux just blurted out in an interview. No one was going to waste precious development time on randomized growth of a tree (non-randomized would have been unsatisfying, everyone would have the exact same tree in every playthrough then).
Which is kind of too bad; if they had you plant it as a child at the very beginning and somehow justified the bandits/marauders at the beginning not burning it down, then had you carve your initials in it as a teen, it would have been a neat little 'look how things have changed' thing by the end of the game. Kind of like in Fallout 3 when you see the picture of you and your dad again at the end. More so if you took evil paths in those games because it would remind you of the more innocent times before you became a monster.