That's basically the same code I started with. The only real difference between your example and mine is that in Functions::Alternate I chose not imported the functions I was replacing to avoid redefine warnings, where as you chose to import all functions and quiet the redefine warnings. I must admit though, your slant avoids having to manually keep track of what functions have been replaced, which is a nice touch.

But if you read down to my reply to rir you'll find that this approach fails when functions call functions within the same package

Consider this:

sub func1 {
  print "goodbye";
  func2();
}
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If func1 isn't also replaced, it will execute Functions::Base::func2() when it's called, not the Functions::Alternate::func2() we're trying to replace. I never realized this when I started the post.