The BKB Super Mod has a Jewish Master Merchant agent unit available to a few factions but I've never built one so I'm not sure what they do.

The Super Mod has more new units overall, but both mods use the maximum possible in any one game (or what was thought was the maximum at the time). The Super Mod has three different maps, one for each campaign game, so GA mode isn't possible. XL uses the same map so you can use GA mode if you wish.

The Super Mod also has some extra buildings, e.g. Axesmith. A lot of the new units/factions appear in both mods but with different artwork/animations.

Although they cover the same ground, they are both excellent and in my view sufficiently different to warrant playing both.