My chain is .flac (foobar2k w/ WASAPI)-->USB-->Audinst HUD-mx1 (DAC only)-->RCA-->Schiit Asgard
To be fair, my Asgard isn't arriving until tomorrow, so my chain currently ends with the Audinst unit...
MP4 is typically a video file, so I'm not sure what you're meaning to ask there. If you mean MP3 (lossy) v. a lossless format, then yes, there is a difference. The amount of difference really depends on the ear of the listener, though, and the quality of the mp3 file (high bitrate v. low bitrate).
Id have to check when I get home, but I'm almost positive that my Apple Lossless files show up as MP4....don't quote me though.