The difference between their ratings is miniscule, and Faf will jump past as soon as the current test is done.
There is a tendency to completely discount performances vs minnow nations but it's somewhat unfair. The innings ratings are discounted because of the relatively low quality bowling attacks (although with shakib bowling a lot of the overs I would argue that the Ban attack isn't completely hopeless), but those runs still matter.
Another thing to note is that since Hamilton has barely any history of good performances, his current rating is more precarious than say Cook's for example.. Cook has had a whole year of poor performances and he is still rated just below Hamilton.
Hope that gives some explanation of the reasoning.
On whether I consider Faf's career to date to be better than Hamilton's - just check the Best Test Batting Careers list.. He's already made the top 100.