But the main app is tightly integrated into the win32 api--moving it to linux would basically require a complete rewrite. DEADBEEF is an example of something like this. Parallel values and ideals, but open source.
There are wine-bottled versions out there. Of course, whether or not output is bit perfect would depend on the wine settings. Bottling it, of course, defeats the point of the program being highly modular/extensible.
Also, you have to remember that a lot of proprietary formats have proprietary encoders/decoders that are incompatible with the GPL.
Shipping Windows binaries are much less of a hassle for the dev than than trying to reverse-engineer everything they need or figuring out how to manage dependencies with different licenses across different package managers and distros with different goals.
tl;dl foobar2000 is an excellent sum of its parts; like Winamp was back-in-the-day. You start changing parts and you get a different sum.