The modifier effectively doubles every modified cart.
The time it takes to modify a cart is higher than the assembly time (30 min for a small module).

Haven't look at the time, but I'm guessing it's a balancing thing.
The modifying itself have been fixed in dev

The modifier have been fixed in a release build and I don't notice that assembling takes longer when modifying a cart, it's always the cost of the hull and then it depends on added/removed modules