I have played a lot of From the Dephts and in my opinion the first option, building turrets and weapons out of mutliple parst, is not a very good idea:
I looks like you have a lot of customization potential, but you haven't, because there are only a few combinations that are good.
Also, it cost simply a lot of time to build the entire weapon system which isn't very fun for me.
You should be able to build the turret itself out of voxel and than place the weapons, magazines, etc. on it, not every single part like in FtD.