Don't you put your ships on FRD when you clear a system anyway? I don't use auto-FRD on military because I generally don't want them on FRD all the time. I guess I'm not clear what the situation is you are describing.
For me, I attack a system and use a lot of Attack-Move (X) while clearing it. Once I have it under control, I'll normally FRD my fleet ball right next to the newly constructing Command Station. You want to set the proper staging location of FRD units anyway, so you at least need to move them to the right spot. Why not hold down V when you do that? It almost seems a "default movement to FRD" would be preferable, where holding down-V is required for a normal no-special orders movement, otherwise you get FRD unless you've selected an incompatible movement mode (say X).