KLA and RMA are based off the Federation Commander game and are not a direct port of SFB (if I remember my discussion with Dan back in June 09).
Further, in my own humble opinion, the problem lies in SFB. I enjoy SFB. But Starmada is internally consistent in ship construction, while SFB is not. As Cole said way back in 1979, it's a little hard to create a real-world battle simulation off a 100+ hours of television film and a few blueprints by an architect. As far as I know, SFB never had a published design system, so shoehorning more and more weapons and systems into the same basic hull became a way of life (in real-world navies the term is "squeezing too many quarts into a pint pot"). Steve Cole himself mentioned in early designer's notes that he liked smaller ships with more weapons and that's the way SFB headed.
In SFB, turning a D6 into a carrier D6CV involved removing two phaser 2s and adding 6 shuttle bays. No SU calcs, just a fiat. (Does a phaser 2 installation REALLY consume the same volume as three shuttle bays? How about a Phaser 1? And if a Phaser 3 can fit on a shuttle craft leaving room for 8 people, a rest room, galley, and transporter...why does it consume even one system box on the SSD of a 500 meter long starship and take a half power point to fire? And just why is a Phaser 4 restricted to starbases? Because it's too big? But 14 phaser 1s and 8 disruptors have no trouble fitting on the GomperStomper dreadnought?)
Want a Constellation-class command cruiser? Well, add a couple flag bridges, couple all-arc phaser 1s, and bang, you're done. There was no real consideration how you fit all this extra stuff into the same size hull. I guess they took out the swimming pools and discos (swimming pools were actually mentioned in the original Designer's Edition (tongue in cheek, I'm sure)).
Anyway, since Starmada (and Full Thrust to a lesser extent) starts with the concept that Things consume Space, and Things' functionality is proportional to Space consumed, you're bound to have some misalignment with SFB's "wishlist" ship design.
I'm not sure why Dan felt it necessary to "fudge" the ratings for the Starfleet ships. I'm guessing essential Starmada calcs ended up having the core "cruisers" (Fed CA, D7) being very unbalanced while SFB maintains they are roughly equal. Anyone tried making a Fed CA vs a Klingon D7 using plain vanilla Starmada construction rules?