Thank you for the additional tips! Also it is not my intention to discourage other users interested in the product, but rather an attempt to help other users with the same issue or point out new issues you may not have encountered yet. If we can identify the weaknesses and improve upon them everyone benefits. I get why you would be skeptical of one user reporting issues others have not, I encounter that daily at my job haha. Perhaps there are others, but they've encountered and solved the issue without saying anything here. If you're another user reading this who encountered the same issue, do NOT throw away your "broken" modules and continue reading!
So, after inspecting the entire module for a couple faulty keys I finally found the culprit.
It's not the legs at all, it's the little plastic cap that secures the metal part to the beam barrel! I was relieved to find the cause, I could finally move on to repair and prevention.
See the attached photo for reference.
The problem: In the manual, there is a disassembled module that looks a little different, but structurally the same as mine. In the manual, this plastic part is much thicker than on the modules I have (as well as a different colored o-ring & a metal washer but maybe that module was a prototype or something). It seems somewhere along the line the spec for this part has changed from that original pic in the manual, or maybe it's a manufacturer issue, or maybe the photos are playing tricks on my eyes. In any case, this thickness is key - these "caps" are very fragile and under the tension of the metal part in an assembled module,
it's enough force to bend or even break off the edges where the metal pushes against that cap. I took a flashlight and closely inspected other modules in my board, all in all about 10 more keys had plastic bits where a stress crack was forming or already formed, leaving a leaf of plastic hanging on by a thread (see other photo for broken off pieces.)
How to fix: Removal of the problematic module is needed, but if you're careful, full disassembly can be avoided and save a lot of time. I doubt many people have this tool, but I used a watchband springbar remover. It's fully metal, long enough to reach into the module from the beam flipper side (while holding the module upside down), very thin, and one end is slightly forked. Absolutely perfect for the job required.
If you dont have this specific tool, try a toothpick or something else that is sturdy, thin, and long enough to get into the module from underneath.
I angled the module to expose the plastic bit about to shear off, and lightly pushed against the broken bit until it flaked off. Flip the module right side up and give the stem a couple taps to get the debris to fall down. Take care to not accidentally break off the entire cap as you "clean off" these flaking bits, it seems like the metal part won't be able to stay on if it completely breaks. I did not come close to doing that for mine but I could see a heavy hand going too far. Also, the stress line from the weakened plastic caused the break to occur cleanly along that line. Now unfortunately my module is not "whole", but I'd rather have a still functional module than using a spare due to such a tiny fault. Truly the most annoying part was painstakingly inspecting each module while they were in the case to look for hairline cracks and figuring out which key they belong to, then flipping it back over to find the corresponding keycap and removing it, then flipping it back over! And having to screw and unscrew the metal plate+PCB to keep the modules in place as I flipped it over each time. If you are feeling risky (and I highly advise against it) you
could just hold the module plate, PCB plate, and PCB tightly together as you turn it over. I tried this once out of impatience, and while everything turned out ok for the most part, I jostled some modules out of place and also accidentally managed to dislocate a beam flipper for a module I had not removed the keycap for, forcing me to turn it over AGAIN and then remove the keycap and the affected module. Whew.
Take care to not push in the bottom of the beam flipper while handling the module upside down as this can cause the metal parts connecting the flipper to dislocate, full disassembly & reassembly is then required!.
Prevention: Well, unfortunately there's not a whole lot one can do to prevent an incredibly thin piece of plastic that undergoes constant movement from developing a crack and breaking, but once adjusted you wont have to do it again for the same module as there is no longer any plastic resting against the moving part!

What one
can do is inspect their modules as I did and look for modules that have cracks already, I highly recommend getting ahead of the issue so you don't have to take the board apart 10 times in a month.
All in all, not every module suffered from the issue, but plenty enough did that I wanted to check every single module, not just those showing an error in the diagnostic tool. Over enough use, as the plastic is exposed to pressure over and over, I'm sure it's an issue I'll have to address again.
Last I'd like to thank Ellipse again for an incredible passion project, and have a couple questions:
1. Could your manufacturer make a slightly thicker plastic cap for the beam barrel part B where the metal part is attached? I'd hazard that a couple extra millimeters would do it.
2. If the above is not an option, is it possible to sell just that part? It's the most fragile piece in the entire module, so it'd be convenient to buy extras of the piece most likely to fail instead of whole modules.
TL;DR The plastic that secures the metal part to beam barrel part B is too thin (at least for my batch of modules) and the tension caused by the bending metal is enough to weaken or straight up break off bits of plastic, causing them to eventually fall down onto the PCB and cause input detection errors.