A couple of things regarding Champions.

[Thalatta]

First, champions is quite a misnomer. One would be hard pressed to find elite troops being called like that in any serious source. They are usually called, well, "elite". There's of course the issue that ranks are "Basic", "Advanced" and "Elite", the first two again terms that one will basically never find to describe how experienced units are. I think better would be "Recruit", "Seasoned" and "Veteran", all terms I've come across multiple times in sources.

Second, what about ships and engines being able to be "champions"? One could make use of elite triremes for Athens for example, instead of making up things that weren't characteristic for them. I guess the main point of champions is to indicate that organic units do not work, but I think there's also a "good unit" implication being made that could be useful for a few inorganic units (they could also have some particular restriction or characteristic, like auto repair? Repair only at Dock/Arsenal? No repair? Whatever is balanced).

[Grautvornix]

Just some very basic consideration (non historical of course): My first reaction was "Anorganic entities like ships or siege engines actually cannot learn, which is the basic conditions to move upwards on the elite training ladder", but the crews operating them can and these are in our case part of the virtual anorganic unit. Like, a good artillery or sailing/rowing crew can move quicker and aim and hit targets much better than newbies.

Therefore it does make sense.

I believe, auto repair (self-healing) is something that would realistically be feasible only ashore for ships, e.g. at a shipyard at best - and it does cost resources (wood and metal). For siege engines there were no depots, instead I guess they were built near the battlefield. So repair is done by other units.