Bosses can be tweaked by adding enchantments and by adding/removing valid armor sets for the bosses.
Armor Sets are a combination of items for each equipment slot of the entity. Each set has a level. The higher the level, the higher in the sorted order the set will go. By default, the provided armor sets have levels 0 (chain), 1 (gold), 2 (iron), and 3 (diamond). The levels of added armor sets do not need to be in order, as at runtime the armor set list will be sorted so there are no gaps between the levels. Each boss is assigned a level when generating, as determined by the boss level up chance in the config. Some types of monsters, like spiders, will not have their armor visible, but will still be strengthened by it.