> The only thing I could find was the trees.lua file in default folder. That doesn't seem to affect mapgen though. I'm guessing it is used only for growing trees from saplings.
Correct.
Mgv6 mapgen trees are hardcoded in that file linked above.
However trees in all other mapgens are added by the default mod as schematics using the Biome API, which means you can write a mod (depending on default and flowers) that does 'minetest.clear_registered_decorations()', then re-register all decorations (including flowers) but with your changes and using your own schematics.
Create your tree schematic files in this way
https://github.com/minetest-mods/saveschems