It does not work on FLAC directly. What SAM does is to decompress on the way in, process in 32bit and compress on the way out (if you select that). SAM generally does not change the original files in any way, a very good thing if you want to certain of not changing the originals.
Generally I keep the original files, do all processing and once totally finished I write to new files. This is a very different work flow compared to other programs that writes even small changes to the original files as default. Makes a lot of sense for taping people. Allows you to test fade-ins, EQ-s, compressing, whatever, tweaking parameters while listening to the result.
It currently does not seem to support several files in one FLAC library, and in the limited tests I have done I have not been able to includer markers.
// GUnnar