mkvtoolnix is using ruby only at build time, rebuilding it after changing RUBY_TARGETS is pointless because none of installed files will change. I think using ruby-ng.eclass is wrong, it would be correct to use something like python-any-r1.eclass, but it seems there is no such eclass for ruby. Please restore old behaviour of mkvtoolnix ebuilds.
Fixed in the tree by using internal ruby hacks instead of the ruby-ng eclass.