Long Live the Confederation!
Never noticed the holes in the plating in-game, and I actually flew my arrow into the gunbarrel on the second playthrough just to get an idea of the size of it.
Yeah, they're "painted on" in the game... so they just seem like big red hull sections. You're supposed to be seeing 'in' to the ship. (Similarly, you can see on that large render that the spots and dots on the Behemoth are actually places where armor plates haven't been installed yet...)
I think the reduced power capacity of the Concordia in SO2 and the general decommissioning of the Confederation line because of the PTC are separate issues. I can't recall the reference for the decommissioning - I thought it was in Star*Soldier, but it's not. Perhaps LOAF can share some insight on this, please?
Yes, I'm sorry, there is a lot of confusion about this issue.
These are, indeed, two separate things. The scene in Special Operations 2 is Tolwyn ordering Angel to fire the gun before it has been properly charged--that's the danger.
The thing about ships being decomissioned and so on is very overblown. What people are referring to is a line added in the Kilrathi Saga manual to the description of the cannon itself: "Continual problems with the phase-transit cannon led to its retirement in late 2665." This is NOT saying that the Confederation-class was retired or decomissioned or anything of that sort... just that the gun itself was "retired." It's up in the air exactly what 'retired' means, since we see the Concordia using her gun in 2667... but by the same token we know that all Confederation-class ships didn't suddenly go to the scrapyards.
(The line was added to explain why phase transit cannons aren't around after WC2; a simple retcon to quiet everyone wondering why all capital ships aren't built with them now.)