It might be that pbfs are stored inside sqlite? The whole thing is really incredibly confusing to be honest.
What I can tell you is that my vector slippymap XHR is requesting .pbf files, so that would definitely imply protobuffers as the wire format. Ultimately that's using t-rex and mapbox-gl.js, so... not sure if there's something intermediate. But the mapbox docs say sqlite? I'm just very confused now.
Yep, versus https://docs.mapbox.com/help/glossary/mbtiles/ -- I had them backwards. My confusion might have been because of the name similarities (mbtiles vs mvt), which took me 3 tries to even just type correctly.