It takes more time to coordinate while non-pilot is a captain I believe.
Because when a team captain wants to focus on the specific ship you have to tell your pilot which target he should focus and then your pilot have to tell the crew which side he will take to shoot (on junkers, galleons, squids for example). If pilot is the captain, he only needs to coordinate the crew.
If your team wants to focus on one enemy ship then someone from your crew have to tell you that (in most cases pilot, because there is no time for engineer to look around in tough fights) so you can inform other captains about that. So again if a pilot was a captain he can easly look around, make decision, inform other captains and coordinate the crew.
When I am playing engineer I sometimes really have no time to stay in one place for longer than 1 second (except when I rebuild things, but then I still can't look around battlefield) I don't imagine repairing, listening to other crewmembers, listening captains, talking back to them and giving orders at the same time.
Anyway it's all about preference, but you should have in mind that every second counts in this game.
Correct me if any of my statements are wronger than my grammar.
My position to captain effectively relies on the 2nd mech doing his job well.
Luckily communication is rather easy with a long range ship as I direct him to locations and firing wise he communicates with the gunner regarding effective arc.'
Ultimately I agree with you but with my current mates, I'm the much better sniper (since I intentionally destroy the enemy weapons and engines on a shot to shot basis.) While my pilot is a really good flier he isn't comfortable being the captain or technical guy so until then I've taken up that position.
Hopefully in the near future I can take pilot as captain or the current pilot becomes captain. Like you said, as we get to higher lvls of play, every second counts