Customizing loadouts in Destiny-speak consists of collecting the tools that can cover your relevant bases as a player so that you can swap weapons and armour to mix-and-match whatever range and mod selection coverage you want. Changing the element affinity on armour was added as a sort of drop-protection system so that players really only needed to worry about the stats and not if it also has the right element. The game doesn't really 'punish' players in this short of not having a feature to save preset loadouts.