When you specifying CONFIG_PROTECT="/etc/some_customized_dir", you are actually protecting "${EPREFIX}/etc/some_customized_dir". I think this should be documented or it may be confusing. Reproducible: Always
I've added some remarks about it in the man-pages. Will be released with the next release of (Prefix) Portage.
(yay, use new "in_progress" state)
released in 2.2.01.19120