If you have access to SQLite in your desktop application then there isn't any big wins from using PMTiles over MBTiles; PMTiles does have some special design around tile-deduplication but this is possible in MBTiles too by using table views.
There isn't a tool to do that right now. It could be a fit in either https://github.com/protomaps/go-pmtiles or https://github.com/protomaps/PMTiles/tree/main/python - the Go program is faster and more production ready at this point. I imagine if folders are working for you the quantity of tiles doesn't number into the millions, so the Python program might be sufficient.