It's literally like my comparison of ranked gamers to marines. If you think about it, fighting in a ship is very similar to a video game. Sure, there's some risk of danger, but the stressors of this danger are somewhat removed.
The sectoid views, in my head canon, ship fights like a puzzle, emotionally removed, like a game. And since this is almost entirely a cerebral process, the sectiod has an edge. Compare this to the dumber, more animalistic mutons, and they aren't as good at such calculations, BUT, are better at primal, instinctive reactions, the "do or die" response, also associated with higher bravery. General physical fitness also applies, a muton is in athletic shape compared to the pudgy sectoid, and pure fitness alone would probably add some edge.
In short, sectoids aren't actually acclimated to combat like mutons are, more shakey from fear as they better grasp mortality than the very primal mutons, which makes them nervous, while also suffering a more frail body less capable of quick reactions.
You could also make the comparison of a jock in dodge ball / nerd playing Mario. Both are good in respective jobs, and both involve reaction time, but the jock, less acclimated to Mario would be worse, while the nerd would be less reactive in dodge ball.
Tl;dr, i think you are assuming reactions apply across the board, rather than differentiation of reactions in front line combat, and reactions in the "relative" safety of an incredibly strong ufo hull, which is also semi equipped to survive crashes.
I guess you could say the sectoid is impeded by its nerves in reacting, or that the unpredictable nature of the battlefield makes them less effective at reacting. Overly linier mindset and all.
I also may have other ideas... Perhaps a self destructive core inside chronites making them explode on death, and possibly waspites hatching into bee swarms on death. Or just releasing acidic spores which make any non waspite turn into a hostile fungal mass if it kills , immobile, but shooting more spores similar to a silacoid, very low range and very innaccurate, but extremely dangerous in close quarters. I think this would be fitting, since waspites were so damn fragile in fmp.
