There is add_beskills field mentioned in your post about class traits, which should in theory add BE skills. In reality though it does nothing but exists in the code, and probably should be removed.
I'm also confused about the mod field for class traits. We actually almost removed it from normal traits because we have a much better one, mod_stats. It only remained for special stats like upkeep and disposition.
However when I see stuff like
"mod": {
"magic": 10,
"upkeep": 5,
"intelligence": 5
},
in a class trait, I can't help but wounder how will it work, since the mod field used to apply 10% of stat every 5 levels when we used it for normal stats, thus rising upkeep infinitely.
Either way, there should be consistency in traits. If mod field only increases once special stats like upkeep for normal traits, then it should do the same thing for classes. If we have support for mod_stats for normal traits, classes should support it too.