It turns out to be uglier than I thought, because what Location and Directory locations that mod_perl decides to "upgrade" to their Match versions is random. Actually, we've found it to be consistent in Bricolage (the relevant source code is here). That is, although we can't predict which directives mod_perl will "upgrade", it does tend to "upgrade" the same ones every time. This allows me to check the mod_perl version and try to do the right thing regardless. Maybe we'll require mod_perl 1.27 when it finally comes out.
But at any rate, I'm glad to have the thing addressed and understood. It's not common that I notice a bug in Perl or mod_perl, and it's rewarding to see someone pick it up and address it quickely. Thanks Salvador!