I’m testing my memory here but back in the Squeezebox-only days when I had DX2, there was a choice for which type of file your ripped CD would be stored in on the DX. AIFF was one of them as I mistakenly chose this for a handful of ripped CDs done on the DX. Sorry, I can’t offer any recollection as to FLAC and AIFF comparisons.
On another note, in terms of power supply and kennyb123’s point, wasn’t the whole point of the hybrid linear/SMPS power supply upgrade in the CX/EX to make it “faster”? The proof is in the listening.