When you test your modules, don't test if the prerequisites work - your Makefile.PL should test if they are available, and their specific test suites should check that they work the way they are expected to.
So just test use_ok 'Your::Module';.
(I know that doesn't answer the underlying question of how to test module loading; if you just want to silence these warnings, use no warnings qw(redefine prototype);)
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