<totally...>
I like the idea of uniform placement. This would not only be convenient for text-editing mdls, but could also lend itself to procedural mix-n-match.
On the texture size, I'm kind of itching for an atlas at 512; but I understand (I think) why that's not a good fit for trees. Bear with me for a bit, just to put my thoughts down.
First impulse was make a 2x2 atlas of the seasonal/growth variation - bare, spring, summer, fall. But, really, you wouldn't normally be mixing seasonal variations in a single mod at the same time so any benefits of a atlas are largely wasted.
Second was a per-species atlas with trunk, foliage, flower, fruit. But again some of that is wasted "bandwidth" in that fruits and flowers wouldn't overlap so much. The bigger problem would be the trunk tex is tiled and the rest are decal. So the trunk *should* be single regardless.
Third iteration (after some expensive refreshment and an old man nap) is the trunk single and young foliage, old foliage, flower, fruit atlas would be pretty cool.
I *do* like my atlases ;-)
For size, a 512 DDS would give you the pieces your looking for at 256 and the option for the engine of LoD.
And square is good.
Though 512x256 wide rectangle for trunk might be better :-) Circumference = 3.1415* height, you know :-) <what?>
Edit: Er, girth = something wider than... <*face-wing*>
Oh, shut up, Bird. Let me drink my coffee... <heh>
<...square>