Here is a MoTeC close-up on an upshift and a downshift with manual sequential transmission and no clutch pedal (DFGT wheel). Each dot on the horizontal axis is a physics frame (60 per second).
Upshift:
Downshift:
On upshift, the throttle is cut off until the engine RPM have dropped far enough (depending on the gap between the gears, I suppose). We can also see that the drive wheels (the rear ones in this example) increase in speed during the shift, probably indicating a partially engaged clutch.
On downshift it appears to be the same, only inverse. Instead of a cut throttle it's blipped, and instead of the drive wheels speeding up they are slowing down.
@cjr3559 Could you export an H-shifter GT6 replay to MoTeC, so we can compare the graphs?
Edit: Interestingly, it looks like the autothrottle might be linked to the clutch position during the shift. In the upshift graph there is a small bump in the throttle graph in the 4th frame of the shift, and in the same frame there is a corresponding drop in drive wheel speed. It appears to indicate that the clutch is slightly less engaged at that point, which would transfer less of the engine's momentum to the wheels and slowing them down a little (as their speed is slightly faster than the road speed).
In the downshift graph there is a similar pattern in the last frames of the shift, where the throttle drops slightly, and it looks like the drive wheel speed might be rising a little at that point, although it's harder to tell because it's a more turbulent line than in the upshift graph.