You need to buy the C-Store Retrofit (Tier 5) of the ship to get the requirement of 1 FSM.
Like say, you bought the Galaxy Retrofit (Tier 5 C-Store Purchase) for the Feds..and then bam....1 FSM for your Fleet version.
The K'tinga does not have a C-Store version that is Tier 5, so you still get 4 FSM for your purchase.
I was pretty thoroughly annoyed about this too; I already own a Scourge Destroyer so why can't I just upgrade it to the fleet variant? 2000 zen (or several millions of EC) plus 20k fleet credit is ridiculous.
No discounts at all for KDF is hugely disrespectful to the player-base, more so considering the abandonment of the faction already.