this is an interesting thread, I have not read every single response in detail but my take away is that there is still no unifying definitive diagnosis.
fyi I am a physician, I do emg/ncv testing, I have corresponded with Katie Compton some years ago, I have 23andme genetic data from chip V3 (960,000 snps and V5 640,000 snps and no hits for a genetic mitochondrial defect to explain these symptoms and I have found no definite unifying answer/diagnosis.
most mitochondrial diseases have no treatment anyway, so it seems likely a futile effort, and mitochondrial disease is very unlikely in a patient who can otherwise reach a very high level of fitness.
I think most likely what is happening is the fact that cycling only loads the muscle in a concentric fashion, and the muscle is adapting to the concentric loading of the cycling motion, at the expense of the muscles ability to tolerate eccentric loading, such as running or walking downhill. this intolerance of eccentric loading is the only unifying pattern I have and seems to hold true for most of the posts I have read in this forum.
now without getting to far into the weeds of muscle physiology, you can review actin/myosin and the mechanism of how they work together for muscle contraction and relaxation at the level of the sarcomere, interestingly an ATP is required to release the myosin head, maybe this is related or not. the lack of ATP to release the myosin head is what causes "rigor mortis".
so lets say there is some discovered genetic defect, how likely is it there will be a treatment to fix it, I think extremely unlikely, so all your left with is supportive measures, different training, etc.
one option is to quit cycling, I did for a couple of years and no symptoms ever. if you want to keep cycling, the most effective strategy I have found is to be sure and give the cycling muscles some eccentric loading, before a rest period. the easiest way to do this is lunges, sometimes just your body weight is sufficient, if not you may need dumbbells of various weight as to increase the amount of eccentric load. with some trial and error you should be able to figure how much lunging or even squats you have to and how often to minimize a flare during or preceding a rest period. it might be daily, every other or every 3. depending on how quickly your symptoms come on, you may have to lunge after your last ride, or maybe you can wait a few days.
I think there is one area of genetics that might give some insight, which is that for alpha-actin-3. from 23andme I am TT, which means I don't make the protein, this protein is more common in elite power athletes, and it is involved in sarcomere structure. So if there happened to be a high correlation for this protein genotype within this forum that would be interesting, but I won't be holding my breath, lol. around 20% of European ancestry has the TT, and it is present in fast twitch fibers. so if you had this genotype, and had a higher percentage of fast twitch fibers you might be more susceptible to the concentric only muscle stress of cycling. but there is a lot of might and maybe in that statement.
here is a link to a good article discussing this protein.
https://www.frontiersin.org/articles/10.3389/fphys.2017.01080/full