He doesn't necessarily need to be a Mystic simply because he knows magic. Gaspar knows Bekkler, so he must have been from Zeal, or at least have been there at some point. Long enough for his work to be widely known by a Guru. Since everyone in Zeal used magic, that would clear up the magic question if he was human.
I don't think his physical "weirdness" means much. It's the Chronoverse--there are plenty of weird-looking beings (although, granted, Bekkler is one-of-a-kind). What's weird about him is his presence in 1000 AD. How the hell did he get there? It doesn't show him being transported through time, like it does for the Gurus and Janus. Maybe there were other gates that opened during the Ocean Palace incident that aren't shown.
But back to the Mystic thing--the games really don't go into how the Zealians viewed Mystics. We know they employed them to guard the Mountain of Woe, the Ocean Palace, and the Black Omen. But did they view them as equals, or as inferiors? If they viewed them as equals, Bekkler could have been a Mystic working in Kajar, or elsewhere. If not, I don't see how the Gurus could have known him--unless he was disguising himself as a human.
Although the Zealians did have Nus around, who seem to be treated as equals. Has there been much speculation on whether the Nus are Mystics or not?
Ooof, this raises more questions than it does answers!