Funky is far too polite a word for it. I didn't realize that it was breaking sitewide search but it makes sense that it would. The search package assumes everything in the CR is searchable, which is a flawed assumption.
Hmmm...if anyone has time to look into a solution for this at the search package level e-mail me. I won't hold up the beta release for this issue but it would be nice to fix before final release if possible.