The Dilithium store is always available at all times without any kind of entry fee or membership, I can understand why they are priced so much higher.

Fleet store requires you going to the Fleet Vendor that is located on the Starbase and buy it, there is also a cost in Fleet Marks and it have to be unlocked by going over the tiers.

I will say this, the Dilithium Store prices are fine because otherwise people will no even bother with the exchange anymore or leave wherever they are.