Vorbis, MP3 and others modify the spectrum of your samples which leads to weird artefacts as soon as you pitch them up or down (mostly down). You'd have to pump the quality way up for these artefacts to completely disappear, in which case the files will just be as big as their FLAC counterparts.
No, I will never officially add support for lossy codecs inside MPTM files.

(Small print: You can already use MP3 but even that is not intentional)