Have you tried this with a general viewport? Ren'Py doesn't pass ATL events to displayables inside containers, so that may be what you're seeing. Otherwise, if it works with a regular viewport and not the controller viewport, if you can make me a short reproducible code section I'll look into debugging it.
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after just testing with a non-controller viewport, the atl transitions actually DID work to my surprise! so this might actually be an issue with controller support expansion! I've made a Google Drive folder with both the classic viewport and controller viewport versions of my full chapterselect script. figured that a more in-depth look might help better for debugging than a short extract. there's also a folder containing all of the necessary image assets, so that should help as well.
SMALL UPDATE ON THIS!
I've found that this bug ALSO applies to tooltips. For example, if you have a button in a controller viewport, and that button uses both an ATL transform and a tooltip, the tooltip will override the ATL for some reason, and cause it to (again, the same with the previous problem) immediately complete the animation. It seems to skip over the ease/linear arguments specifically.
I also made sure to test this without the tooltip, in which it worked fine, and with the tooltip in a regular viewport, and that, too, works fine. Not sure if this will be helpful to your debugging process or not, but I thought it to be worth mentioning.
I've got it on my to-do! Unfortunately I just have a lot of things to do 😅 But it's in the issues page of my repo. The example you gave was missing a few things for me to make it run properly, but I was able to reproduce a pretty basic example by popping some ATL on buttons in a controller viewport. I will let you know if I have any updates!