I don't want to say the devs are lazy, but it probably takes less work to add or change specs than to design new ships.
I think a big part of it is just to give all players a reason to fly a ship of the flagship class, to fly a ship of the same class as the Enterprise-F. To do that, they have to change up the stats to make it useful to each class. There was a lot of hulabaloo a bit ago about how all new ships are cruisers; I can see Cryptic taking that message and trying to make the new ship reasonably appealling to Tac, Eng, and Sci captains^H admirals. I don't have a problem with this.
Then they went and made a set bonus if you mount the consoles from all three variants. This I have a slight problem with.