I notice this for sure, but there is a way you can get just the right angle where both strokes sound identical, on single notes, that is (this may be at odds with other factors though). I have pretty sensitive ears for this from my classical playing as we strive really hard to ensure each finger makes the exact same tone. So I am confident I am really hearing the difference, just like I’m pretty confident when I’ve attempted to get the tone consistent on up/down strokes, I’m really accomplishing that.
I’ve also got a lot of experience in metal playing, and I was definitely of the opinion that down strokes should be used whenever possible, just like Hetfield. I’d particularly notice differences if the rhythm part had some power chords (which almost always happens at some point in the phrase in that genre). Even if the tempo is fast, when more than one note is present in the part, upstroked chords will sound brighter since the higher note sounds first.
I think this is definitely part of it. Also, if rest strokes are being used, they have a more full sound by default too.