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.
Feel free to open an issue.