I have now concluded my testing. I did all my tests on my Raspberry Pi 3 and each of the four controllers survived at least 72 hours of testing without producing any phantom presses. However, to make one of them stable, I added an additional 22µF cap at position C41.
All of those tests were done with just one controller attached to the USB ports of my Pi. As a last step, I took the controller that was most unstable before the fix and connected it to my RPi3 together with a mechanical USB HDD (Western Digital 2.5"). Unfortunately, this did provoke a few phantom presses. Nothing huge; two phantom presses over four hours.
I guess the conclusion is that this fix will dratically reduce the risk of phantom presses. However, the combination of a fairly unstable controller and a USB port that provides noisy power can still produce occasional phantom presses. I should point out that I’m using the official power supply for my Pi, so it’s not some no-name crappy one. However, since this phantom press issue seems to be very much tied to the quality of the USB power, even just changing to another RPi board could provide different results. This also makes it tricky to verify that a fix is 100% effective. Besides, without an oscilloscope I can’t even know for sure that my Pi’s USB voltage is within spec.
Although I would have liked for this fix to have completely eliminated the issue, I’m still glad it works as well as it does. I admit that I’ve used some trial and error to get my controllers stable and I don’t doubt that a more elaborate investigation (using an oscilloscope) could provide a better fix (probably involving adding smaller caps as well). However, I’ve already spent too much time on this, so someone else will have to do that.