My logic was that the main limiter on acceleration is inertial dampers, so strictly speaking even the largest ships should be able to match a frigate in straight line speeds if they have the same thrust/mass ratio, because the upper acceleration is fixed. But thrusters aren't as strong, and the more mass there is the more force you need to redirect to adjust course, so the same RCS system can produce much faster changes in attitude and course on a smaller ship than a larger one.
But yeah that mass is outscaling the costs for engines and whatnot probably means that in the TMP transition there needs to be some consideration given in regards to building an engine calculation based on inertial damper maximums and RCS power from first principles, not just caveman bonk rock number on other rock number. Which describes a lot of systems under the hood, frankly, but I've always been doing this on the fly and this initially just started as a kitbash/art quest. Feature creep is definitely at play.
Fortunately in about 70 years phasers can be converted to a length-based/power system, which I expect will deal with a great deal of angst.
Funfact, this initially started as an idea for a Stargate Prometheus design quest.