As you note, this plugin should be below Battle Engine Core. As for the casting animation issue, I've never noticed this issue, but I'm not using Yanfly's ATB for my main project. I have a lot on my plate, but I'll check it out when I have time.
EDIT: It's not ATB that caused it. I think it's from a change from post-3.0, as my main project was still on Dualtechs 3.0 and doesn't have the issue.
EDIT 2: Just a stupid typo in the code. I'll upload version 3.1.2 shortly.