YF12 was certainly flying at that time. Only an assumption, but I would have imagined the extra weight of a WSO and associated systems, plus larger radar, missile bay apparatus would have impacted service ceiling.
Also, there was an aerodynamic penalty from the larger YF12 nose section - to accomodate the radar - necessitating the addition of ventral strakes under both engines to control yaw.
Personally, I find it sad to look at those incredible pieces of engineering and photos of Kelly Johnson, Ben Rich and others - and think that the challenge of absolute speed and height in manned aircraft seems to have taken a backseat.
I wonder if we will eventually learn more about Isinglass
- and if there were/are any real high speed manned successors (rather than the mythical Aurora).