Hi,
I've installed v4 yesterday, through Steam and using modmerger as well, and upon character creation, I noticed that none of the changes made by the anthology appeared. It was just BG:EE without modification.
I've haven't checked for the other changes so far.
I believe I've seen a similar problem in a thread from 2016 and Camdawg asked to see the debug file. I don't know if it has resolved anything, but I'll attach my debug file here, nonetheless.
Thanks in advance!
SETUP-CDTWEAKS.DEBUG