So, I found out more about it. Firstly there is no Legendary or Divine item generation. At level 9 and at level 16 all newly generated item rarities are displayed with increased rarity (by 1 at lv9 and by 2 at lv16). That is also the reason uncommon and rare vanish at these stages.

But there is an actual bug! ItemTypes.txt will always only read the last entry. All other changes are ignored. Because of that I had to create separate mods for each stat. I tested it in and out, it does work this way and not if put together.

Here is the mod I ended up with (increases rune slots):
http://steamcommunity.com/sharedfiles/filedetails/?id=1188085656

Will this bug be fixed?