The end goal of PMTiles is similar to SQLite-over-HTTP: SQLite is designed for access on local disk, and might make many requests for a single query, each incurring a HTTP roundtrip (could take hundreds of milliseconds). PMTiles is designed from the ground up for HTTP, so attempts to minimize the # of requests to 3 or less for any tile.
The extra conversion step is something I'm hoping to get rid of by building PMTiles writers into tiling tools directly.