Well...yeah... they're there because you can for instance bring in dirty completely asynchronous signals from timers, general port pins (via events), or direct LUT inputs (on applicable port pins)... there are many places you would want that feature.
Indeed I'm using that on this very same project, as part of a sigma-delta decimator which works very nicely; synchronization is required, else the count shifts by a bit position or so, +/-, due to temperature dependent delays in the external signal path. A perfect example of using it.
But that's inapplicable here... the whole point is the race condition. I measured it myself, I saw the waveform, it fails to trigger following an approx. 1-cycle-low pulse. This is completely after all the sync and filter stuff, at the f/f output, at the LUT output, on the event routing that signal to -- in this case -- the ADC event input AND the port output. Give or take internal propagation delays, I suppose, that's entirely the beginning and end of what the ADC is seeing. It triggers on the rising edge after longer low-pulses, I saw pulses of several clocks in duration triggering normally.
It only fails on the narrowest pulse. And it doesn't trigger at all on a "zero" pulse ("forbidden" state), I don't know why they don't say it's R or S dominant. The result is simply no state change and it waits until the next trigger, functions as intended.
I don't get... what's your point here, look, I described the situation, the only thing left to do is test and confirm, or otherwise modify to get a minimal test case. I read the datasheet, I did the measurement, I removed the race condition and it works reliably, you're just speculating on cause..? I get wanting to be helpful, but the OP isn't really a question, it's information in need of confirmation. Not trying to be rude here, but this is beyond the stage of pointing at the datasheet and hmming loudly, additional "hmm"s aren't being helpful.
I do appreciate the thread-bump though; perhaps someone with some free time and an AVR-DA will see this and give it a spin.
Tim