The starting plot code evaluates an area larger than a single city which is why deserts score so low for most civs. For your map specifically you can see the effect of a couple of things happening;
1) The clan was likely placed early, perhaps as the first civ by luck of the draw. Since the clan does well with early wars they have a higher neighrbor value so they 'cut' fewer surrounding start location which allows other civs to start closer to them than normal.
2) Start plots are taken from a list of potential city plots, those are valued by food, commerce and production with no regard to civ preferences. That list is then pruned down so that only the best half of the potential city locations are kept and then finally, the civs pick what they like out of that list. While a floodplain start is ok for food and if you're lucky to have gold you can do ok for commerce it's very likely that the desert is surrounded by plains (not so good for food) and peaks (not so good for much of anything). Desert hills are also the worst hills in the game and tend to be present near rivers. So typically there are only a couple of available start plots in the desert for the civs to chose from in the first place and the greater area around them will generally be rather poor.
3) You have flavor mod enabled, doing so can result in civs being shuffled around to places that this script didn't intend them to start on. The clan, for example, should almost never start on a coastal tile. The again, with you and your tiny maps they don't have much choice
4) Also, since you have flavor mod enabled I can tell you that the bonuses you see are NOT the bonuses placed by this map script. I don't like the insane clumping around start plots that flavor mod causes.
5) Finally, you have flavor mod enabled and that completely skips my cleanup for peaks, jungles and forests.
6) Anyway, you'll be happy to know that I have a 'smart climate' option in the works. This will give you the choice to use exactly the climate options you select, modify the ones you select based on the civs present in the game, or set the climate options entirely based on the civs present in your game. So, in your case this code would have reduced the jungles and deserts giving the civs more room to pick a start plot.