BookMacster would not support Waterfox until we've reverse-engineered it, tested it and explicitly coded it into a BookMacster update.  It is possible that Waterfox may end up being just like Firefox except for the locations of the files and bundle identifier of the app.  You are welcome to test the places.sqlite file format by replacing the file as you propose; that would be one aspect of compatibility.  When doing so, be aware that there are actually two other files which you must replace in concert with places.sqlite: places.sqlite-shm and places.wal.sqlite-wal.  The bookmarks database consists of these 3 files.

A little warning: For the last ten years or so, the Mozilla bug database has referred to an upcoming major rewrite of the places.sqlite database which can perform poorly (be very slow) with some large bookmarks collections, and contains orphaned features like tags and shortcuts which are not supported by Firefox bookmarks extensions which were added in the meantime .  At this point, of course one wonders whether that major rewrite is every going to happen.  I am not familar with Waterfox, and wonder if Waterfox has copied the same cruft or done a partial or full rewrite.