Can you elaborate? The choice screen in this template is the exact same choice screen as a regular default project, just with the styling made explicit. You'd need to share this new enumerate and animation code you're adding and ideally how you're testing. I believe I recently saw an issue relating to ATL on the Ren'Py GitHub as well which may be relevant.
https://drive.google.com/file/d/1vKiHhnhVPRcAF_f98zCb3PUqa3fCgAM9/view?usp=drive...
here's a renpy project stripped of everything to make sure there's nothing else that might be the cause.
transform enter(p=0.0):
alpha 0.0
pause p
easein 1 alpha 1.0
transform leave:
on hide:
alpha 1.0
easein 1 alpha 0.0
screen choice(items):
style_prefix "choice"
vbox at leave:
for n, i in enumerate(items):
textbutton i.caption action i.action at enter(n*0.75)
and code case you need it