I often see people write MY package that subclassing ExtUtils::MakeMaker in their Makefile.PL files. Theoritically, we can probably create a method that overrides/extends the part of MM that writes this .yml file. Of course, in order to do so, one needs to learn more on the MM internals.

OTOH, Module::Build directly supports no_index section. You may wanto to consider to switch.