Yes, something serious would be very likely to be making him lame during flatwork, and even more likely after schooling over fence. Not guaranteed, but likely
Many, many OTTBs/OTSTBs have osselets that are cold and set and have high performing careers. That’s because they usually don’t affect the extension/weight bearing aspect of work.
There are many situations where a little bone chip is in a place where flexing the joint hurts, but weight bearing/extending the joint doesn’t bother it at all. Some of those are left alone, as the risk of actually causing a problem with the surgery is greater than the risk of leaving it in place. Some chips need to be removed asap, due to location, even if not currently causing a problem, as something about them makes it likely they will cause problems sooner rather than later.
It’s unlikely to be arthritis, unless it’s somehow like an osselet in that it isn’t bothering the weight-bearing load, but does get angry when flexed, especially if a vet flexes harder than they should (and that absolutely happens).
Not likely to be soft tissue, as he likely wouldn’t be sound for the work you describe. Possible, just not probable. I’d say Beau’s experience is fairly uncommon, but I could be wrong. Maybe it isn’t too surprising, as I don’t know many horses who get flexed for a lameness eval “just because” lol Who knows, maybe more of those would be found before they cause obvious lameness, but I’m not a fan of any regular flexing just to see if something shows up LOL That said, it’s not necessarily a bad idea for a young horse just getting into more work.