iTune will not store FLAC files. It will store AIFF and ALAC files. So, either your FLAC file was converted to one of the above formats or you have a program such as Pure Music that is using iTunes as a library but not storing the actual file in iTunes. I use a Mac Mini and it has the most current iTunes and I run Pure Music. Pure Music will swallow just about anything but I usually purchase ALAC files from HD Tracks because they are easier for a Mac user to deal with. AIFF is full resolution which is a waste of space. I ran a double blinded test with three friends (wife did the switching) And none of us could tell the difference between AIFF and ALAC. None of us could reliably pick out 192/24 over 96/24. I did not have the software for 48/24. Two of us could usually pick out 96/24 over CD. I question if this was due to different masters. The end result is that I buy 96/24 files. My own opinion is 192/24 is a waste of space. The file is twice as big.
Do Macs Play FLAC?
My my understanding was always that they could not play FLAC encoded files. I just installed a Synology NAS. I have a Bluesound Vault 2 with about 300 CDs that were ripped in FLAC and was able to transfer the contents of the Vault 2 to the NAS. These show up as FLAC files in the NAS index. To my surprise, they play on my MAcAir, purchased in in 2013, via usb into a Bryston DAC3. I had assumed I would need a music playing program to make these files playable on the Mac. I have no FLAC converting software loaded onto the Mac