I just checked on it... On a fresh reload (So the distance-to-capital modifier is completely factored out) my max skill (I think he's actually several points higher than max skill actually, and they do keep counting above ten) would get 158 florins from the gold mine he's sitting on in Timbuktu, but only 79 from the mine in Zagreb, so yes, there is a difference in the base values (Timbuktu is the richest region in the game, as suspected--and it's logical enough considering it's utterly worthless in a strategic sense).

With distance-to-capital reinitialized by moving the capital and putting it back, he makes 1088 florins per turn in Timbuktu, and would make 544 from the one in Zagreb.

Moving the Capital to Granada or Toledo significantly nerfs the output of the merchant, but moving it to Valencia less so, which leads me to believe that it's a combination of distance-to-capital and also how built up your capital is (Since Toledo and Granada are castles in my game, and therefore poor trading facilities, whereas Valencia is a slightly smaller city than Cordoba, so I netted almost as much with my capital at Valencia as at Cordoba.

Moving my capital to Timbuktu actually lowered the merchant's trade output below the base value (What it was after a reload) so apparently being too close to your capital incurs a negative modifier (And also Timbuktu is a hick town at the moment... I haven't had any reason to build it up and the population is rather miniscule in the first place).

I then used the console to zero out the skill of one of my merchants and hovered it over one of my gold mines, and it showed that with 0 finance he would make 155 florins per turn on it. Upping his skill to 1, he would be able to make 233 florins per turn.

So as you can see, Timbuktu is a wildly profitable area. I can't account for the lower values you are getting there unless the game considers Caesarea to be vastly closer to Timbuktu than Cordoba (Which would make no sense since the game appears to make all distance calculations as the crow flies), or you are maintaining your capital as a castle, or are just at a lower tech level than me.