Yeah, I kinda expected / feared this, but wanted to make sure we didn’t miss anything obvious.
The split-up idea doesn’t quite work in our case, due to how the elements are composited together, so we’ll have to give up on the EG template and do everything in After Effects as individual comps.
Perhaps Adobe will consider an option/switch to make specific animation tracks or expressions “responsive” (i.e. not influenced by time stretching). Not sure how that could work exactly, but I guess I should make a feature suggestion, maybe others would find this kind of thing useful as well.