I don't think the crafting will lead to OP weapons. I assume each module will slightly modify the gun's stats (e.g. +5 accuracy for a long barrel), and might also have a negative effect (+2 weight). It will, however, allow us to adjust our weapons to our own particular tastes and play-styles. I like scopes on my rifles, and shotguns with quick-load magazines. This crafting system looks like it will be a lot of fun to play around with.
I'm sure you can take or leave it without being heavily penalized, if you can't be bothered. In NV, I slapped a few mods on my favourite guns, but I never really got into making my own ammo. In Skyrim I did a little smithing, but I almost completely ignored making potions. It never felt mandatory to do the crafting stuff beyond what captured my interest.