Yes and no.
Direct dilithium per item cost is less than half of the dilithium store.
You have to pay Fleet credits in addition to dilithium though for the fleet gear and of course need a fleet gear provision which is provided by the fleet.
Getting provisions has costs of its own which is making the fleet gear probably more expensive if you break it down, but I view the provisions as a side effect of leveling the base.
If we ever max it out and concentrate on getting provisions that might change of course