It does have a FLAC>ALAC converter built in that should automatically convert before transferring, but I've found that it doesn't work properly with my mini. The tracks will convert and transfer, but won't actually play.
Being the cool guy I am, I vibe-coded it into something I can run as an app in Linux, so while I was in there having a fiddle, I changed the ffmpeg instructions to convert to a 320kbps AAC mp4 instead. This seems to have worked perfectly.
All in all, it's an incredibly neat solution.