Yes, there is a difference. Two of my amps have the usual B-M-T controls, and also a Presence control.
Technical aspects aside, here's what I noticed....
As I turn up the Presence, I notice my sound gets "glassier" and more up front but different from what the treble does if I turn it up. As I turn the Presence down, my overall sound gets somewhat darker and "kulob".
Depending on my mood, I find the Presence control to be very helpful. With a strat/tele, I turn up my Presence to have more punch and snap and glass to my sound (while keeping the EQ untouched). Whenever I get my LP and play heavier tunes, I roll my Presence down to get a darker and more "evil" tone (still keeping the EQ untouched). Pero when I'm on my 80s glam mood, I like to keep the Presence at noon or just a touch up to get a good sizzle and bite for my high gain tones.