I was going to recommend their mailing list, but I'm not actually finding any information on it. I know I've seen those guys active (arguing the merits of strawberry over active) on one of the lists I follow. (Probably perl-xs?) I'm sure they have a list somewhere. That's definitely where I'd start.
My thinking is that you'll have to argue your way through it. It isn't a bug. They did that because they include a bunch of libs with strawberry, which is part of the reason people like that dist I believe.
You might argue it's a bug in CPAN... It seems to be the various INC dirs (from config and makefiles) should be additive in some circumstances. So maybe it's a bug in EU::MM? I certainly couldn't say. I can think of cases were you'd want to be able to override INC and others where you'd want to add them.