Update:
Took it to the dealer. No water leaks or damage per their eyes. They looked under the headliner as well and could not see anything. He also stated that if it was water damage you would see stains, even on the black liner.
They've gone ahead and ordered a replacement headliner & foam insert (the whole top basically). They'll be replacing it.
Such a weird issue, but glad Mazda is taking care of it.