Aren't you overcomplicating the issue? You don't have to make a big deal out of a small one.
Recently, I also had to take out this pcb, because I managed to break the encoder shaft. I replaced it with a Chinese encoder (a bit bumpy) and tried to put it back in place. I saw that the cable connector is higher than the encoder, which is why the pcb bends in a curve during amplification.
The problem can be solved simply: put some washers or nuts as washers on the axis of the encoders. Do so that they can still be attached to the front panel. That is all. No need to overcomplicate it, this is not atomic physics.
Think in simple terms, then you won't overcomplicate it. Rather, pay attention to the cooling of the device, it should not get too hot and the generated heat should be able to escape from it.
I am slowly reaching four thousand QSOs, for me, I modified the device to remove the generated heat and to set the Bias correctly. Don't wait for hfsignals to solve it. If you have noticed, if not, I will tell you that in the case of uBitx, what you found to be good was not included in the next amendment either. The manufacturer leaves it up to the user how to solve the modification. Read what you can learn from and make the correction.
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Gyula HA3HZ
HA3HZ