It's a little more complicated than that! This mod doesn't overwrite anything, really, but what it does do is create its own "s6xdvt-fake-tree" prototype, which is not going to get the changes you're making to tree-plant so it will seem like your changes are getting overwritten. I actually did it this way to avoid making lots of weird breaking changes to tree-plant because I thought that would be less likely to create problems for other mods, although it seems to have backfired a little in this case! For better compatibility between Diversitree and Early Agriculture (and other mods that change around tree-plant), I moved my own tree creation code from data to data-updates, which will grab the changes you're making to the growth times and mining yields of the trees.
This won't solve the issue with Alien Biomes out of the box, but the short answer is that if you add a line like this to data-final-fixes everything should work fine because you'll make your tile restriction changes to the prototype that's actually getting planted when Diversitree is active.
if mods["Diversitree"] then tree_plant = data.raw["plant"]["s6xdvt-fake-tree"] end
