I'm an audiophile and the difference between the FLAC and ALAC format is significant by listening. Mostly i buy music from Bandcamp and i have 6 options to chose between the formats to download. The musics are uploaded as AIFF, WAW, or FLAC and the conversion is completed automatically to the required format. So it is pretty easy to compare the same song. My conclusion is the ALAC have a better dynamic and clarity, listening songs in FLAC format (even from different origin) is sound flat and distorted in the high mid-range.
The hardware probably have nothing to do with this because 5 different external DAC sitting on my desk, what i built up from the best components i can put may hands on. My relative have the same conclusion on his different gear, and player on his PC. I have a DT990Pro and i sometimes use a T90, but i do not need the T90 to reach this conclusion. (If i have to do a blind comparison on a portable player i bet i loose and i agree format doesn't matter.)
To make it clear, i do not care about Apple and their products, but even if the difference it is based on the encoding/decoding i go for the ALAC in the future and avoid FLAC if there is an option.