Except most of the time, on the average ship, a single Engie COULD manage the important stuff, as long as someone was dedicated to serving as a secondary repair person. Lets use your "problem ships" as an example.
All ships are "problem" in encounter. There are no interest in maximum possible HPS, the repairing-bebuilding-cooldown balance is based on idea you need to be IN proper time ON proper place. That is why we have "responsibility" zones on all the ships, where parts are divided between engineers focus.
Pyramidian: It only ever needs one Engie anyway, as the Engie's entire job is sitting on the lower deck keeping the hull and engines working. The second engie is always stationed at the balloon anyway. This job can EASILY be managed by a Comm Officer, or even a Gunner. The ability to super-repair is NOT a necessity for this. Hell, the Comm Officer takes Mallet, the Gunner takes Spanner, and together they can maintain the balloon and guns, leaving the engines and hull to the actual Engineer.
Fisrt enemy with caffonade or flametrower (or incendiary carronade) will be your painful death. Because destroyed baloon is a HUGE HOLE for hull damage. As well, balloon is most vulnerable to fire, so that it must be chemspayed all the time. So in the situation of real combat your people will not be on guns, but on baloon.
Galleon: Really, the Galleon is a tricky ship even with 2 Engies, so it's a ship that may not want a Comm Officer. However, if one is used, it could be assigned to the lower deck as a Gunner Comm Officer, maintaining the weapons lower-deck engines. Meanwhile, the Pilot actually sets up to help repair the balloon in a pinch, and the actual Engie goes where needed, with the Hull being their primary focus. While two engies could maintain the ship as a whole easier, it's not absolutely necessary. This ship does require more coordination between all the members regardless though.
You have not even invented the new class, but already founf where is it unneccessary.
Spire: A single Engie can actually maintain the entire Spire pretty easily if they know what they're doing, as long as they can keep the armor up. It's possible to hit the Hull with Mallet, drop down and hit the Balloon with Mallet, and get back to the Hull just as the cooldown from Mallet ends, and hit it again to start the loop over. That said, I'd put the Comm Officer on repair duty primarily on this ship, with their role being to repair destroyed parts rather than to keep things alive. Once the armor can be restored, the main Engie can easily use the parkour loop to restore the armor while maintaining the armor on the other part. Fixing broken engines and guns can be shared, with shooting happening whenever. Again, they don't need super-repair power, they just need to not spend 90% of their time on the guns. Even a Gunner could fulfill this role in the current game, if they didn't sit on the guns all the time. While they will obviously not be able to pull the trick the Engie can with Quick Repair then full Armor in a very short time, they can do basic repairs.
I really want to see you playing as engineer, because you seem not to be much realistic.
Basically, let the Engie deal with the Emergency Repairs, while the Comm Officer deals with routine maintainance, buffs, and information warfare. All of which it can do while doing said routine maintainance.
Everyone does emergency repairs. Even pilots. Lueosi participated in rebuilds hundreds of times.
Now, as to what you've said about Pilots. You seem to have this belief that a Pilot, the only person on the entire ship who can effectively fly the damn thing, would lose their role as Captain if the Comm Officer was made.
Good pilot is a leader with 8 hands, who manages setting crew, setting teammates crew, setting good enemy team on opposite side, talking with crews on match, talking with ally, deciding tactics, taking up conclusions, and well, for the last thing he moves the damn thing. Appearance of person who can be in charge for strategy will move a pilot to crew slot. And a lot of pilots will not like it, and decide to abandon the game.