First off, both are lossless compressed formats. Other examples of lossless (but uncompressed )are AIFF and WAV.
So, the fact that one file gets bigger or smaller is simply the compression settings, not the loss of musical data. FLAC, for example, defaults to compression level 5, but is settable by the FLAC encoder/user and is a trade off on size vs decompression times. And yes, I've converted FLAC to ALAC, AIFF and WAV. Most claim no difference (they are each lossless for gosh sakes) some claim some (like me).
I have no experience with 3rd party FLAC on iTunes playback (Fluke or whatever). I use Pure Music and use wav, mostly (which is not a discussion for this thread).