We would like to make sure that mergemaster won't be affected when RCS ID is removed.
My conclusion is that $FreeBSD$ ID doesn't really matter for mergemaster.
For -U, the code basically sets AUTO_UPGRADE, which causes mergemaster to install new file if it's not user-modified (by comparing the current etc/ tree against saved mtree file). It works regardless if $FreeBSD$ is present.
For -F, the code does a comparison with diff -q -I '[$]FreeBSD.*[$]' and installs new version if the file only differs in $FreeBSD$ tag. If we stop expanding $FreeBSD$ or have it removed, the code would fall back to the traditional way of compare and when -U is present, it would correctly handle non-modified configuration files as usual.