Interesting thoughts, duak. (FYI, I forgot to label D1 correctly in my LTspice schematic; it's representing VR6 with a ~4.7 V Zener, which is probably close enough to the real 4.2 V part for simulation purposes.)
No, the meter pointer is in the middle of its range. I'm doing all my testing at 30 V. The meter graduations go up to 50 V. When S2 is in the lower range, it's divide-by-ten for 0-5 V.
I think I see how Q15 is supposed to work based on your description of the current limiter. But what does the manual mean about Q15 setting the bias current for the amplifier per section 4-38? If you disconnect the Q15 collector in the LTspice simulation, the meter voltage drops to essentially zero, so Q15 is still doing something even when in saturation.
I measured Vce of Q15 and selected the 5 V range while driving the output voltage higher. At about 10 V, Vce starts to increase, but even when the supply is set to 50 V (ten times the meter range), it only reaches about 70 mV... so it's still basically in saturation. Now, if I try the same thing on the lowest amperage range (180 mA), Q15
will come out of saturation when the output current reaches 0.5 A or so. Is this behavior inherent to the difference between sampling the output voltage vs. the current sense resistor voltage?
Regarding the dips on the meter curve, I'll pay attention to the airflow in my room. We're using heat now, so there wouldn't be a heavy electrical load from AC, but temperature could play a difference. I can try putting a thermocouple in there and running the test again. Even so, I'd be surprised if it's the furnace, as my lab bench is about 15 feet away from the nearest vent and I had the lid installed on the power supply case. This thing would be super sensitive if a 1-2 degC ambient temperature change caused the panel meter to deflect so significantly.

That being said: for Q12 and Q14, component temperature really does seem to make a difference. I can squeeze one of the BJTs with my finger and the meter input will move by about 200 µV. If I squeeze the other one, it'll shift by the same amount in the other direction. This isn't really enough to see on the panel meter, but when I hit the transistors with freeze spray, the meter input will move by 2-3 mV, which is upwards of 2 V on the meter on the 50 V range... quite visible.
I took a closer look at the 6289A errata (attached) and HP does actually call out replacing Q11 with a dual part in later revisions. Under Change 4, they're saying it's a 2N4045, which appears to be a matched pair with "tight Vbe tracking" per most of the data sheets I've found. That's probably what's in my unit, or at least something close.
While playing around with a few things as I was writing my reply above, I noticed that I can get the get the panel meter to move significantly by touching the components in the meter amplifier circuit. I know the human body is going to have some conductivity, but I didn't expect to visibly see such a change. This leads back to cbutlera's post in Reply #46 about PCB leakage. Might this be what we're seeing with the meter amplifier circuit and any adjacent components?