It's mostly the various forms of lag that cause that. My guestimation (based on behavior I've observed over the past 3 years) is that for the M-mode shifts, the TCM takes a snapshot of your current revs/speed/accel-pedal and decides on a shift-timing and rev-matching strategy to match it, but doesn't update this data as it goes through the process. So if you change the pedal input after it takes its snapshot and it will throw off the results a bit.
If you're trying to force a softer or harder shift, and you nudge the pedal at just the right time in the process, you can have the intended effect flawlessly, but figuring out the timing is somewhat counter-intuitive (again, because of all the inbuilt tiny delays in various systems between button-click and various actions taking place).
I *have* played with D-mode driving from time to time actually, and in general D-mode does seem to cope with arbitrary mid-shift throttle changes better than M-mode does. On the track I have zero issues with this whole M-mode + throttle position stuff anyways though, because if I'm downshifting I'm completely off the accel and into the brakes, and if I'm upshifting I'm generally at a constant throttle position (either nailed to the floor straight line, or some in-between value that's holding a perfect traction balance during a sweeper).
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