Kerbal Space Program

I agree with the OP.
Right now the yaw, pitch, and roll axis groups behave like custom axis groups that just happen to be matched to the same keys as the controls for the craft. Neither SAS nor the manual trim affects the deflection of the axis groups. This is in contrast to the Main Throttle axis group, which behaves as I would expect it: the throttle setting directly sets the deflection of the axis group.
One additional effect is that yaw/pitch/roll values that are displayed in the Mode Control Window during flight have different effects, depending on if the control input comes from SAS / trimming, or from manual control inputs.

P.S. If it wasn't clear: yes, I also recognize that this would mean that "Incremental Control" for these axis groups wouldn't make sense anymore, and only "Absolute Control" is available. Just like it is for the Main Throttle axis group.
P.P.S. Or to not break existing craft one could add a "Absolute Control with SAS" setting. :)

This would be the only way to use automatic stability control for a VTOL craft as far as I can see. Unrealistic that this would not be possible.