In the ENT episode first flight, when Forrest tells Archer the NX program has been put on hold indefinitely after AG's failed warp 2 test, he mentions starfleet has decided to design a new engine from scratch, independent from Henry Archers design. Could this be what eventually becomes the Franklin's engine, developed alongside the NX's by a different contractor, but only ever able to achieve warp 4? Could be why starfleet went with the NX warp 5 engine for their flagship, but assimilated the Franklin into their registery later when needed.