As I read your initial post, I came up with the same idea as shmem. But after some digging, I think there's an easier solution.

Manpage separators are provided by replace_manpage_separator() in each EU::MM_* file. But the method is only called from EU::MM_Unix::init_MAN3PODS(). So you might be able to just patch that file to do something specific instead of calling the OS-specific EU::MM_* file.

- $manpagename = $self->replace_manpage_separator($manpagename);
+ $manpagename =~ s{/+}{.}g; # from MM_Cygwin.pm
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The inheritance structure is hard to follow or I'd suggest something more clever than copy/patch.