Just an aside. Why do Y-Wings have what appears to be windows going all the way back? These are there on the BTL-B as well, they wouldn't be used though, as the gunner stands in the bubble. This would block the pilot from being able to use them over his shoulder (if he can even turn enough to look there in a full flight suit). In the A4 version, the turret mechanism is in this area and would block the view. If the S3 version's passenger/gunner sat facing backwards (like the snowspeeder) then it would make sense as the gunner surely wouldn't be able to turn with the turret, instead using some sort of instrumentation. Having the ability to peak out the window as well, and rely on info from the pilot for the front windows would be reasonable. I think all views we've had of the S3 interior have depicted the second seat facing forward. At least the Rebel gunners and pilots didn't have the same sort of bulky flight helmets that didn't cover as much of their peripheral vison, so they maybe could at least make partial use of the rear windows. There's also no rear or side-view mirrors on any star-fighters that I can recall but those aren't really expected. The only thing I can figure is that the original spec for the Y-Wing chassis didn't have a turret at all, it just had a long cockpit for a pilot and a passenger or bomb-controller. Then the GR added the turret and the success of this led to the variants which included a turret but did not require or have room for a gunner to operate them.
I had forgotten about Chopper's y-wing being the A4/S3 style chassis without the paneling. Either the GR did in fact use multiple variants, or they decided to strip the armor themselves at some point to improve maintenance or lower the ship's attack profile. It also doesn't appear to have any turret at all, which is odd. I'd need to go back and watch, maybe it was removed but the flat panel in the circular area is odd to see in the still above.
Anyway. Back to the topic, I guess I was wrong. They don't really have a lack of options for large ships. There's a good number that could work, though some of the suggested options might be more appropriate on a medium base.
Of those suggested for a large base, the ones that make the most sense seem to be the LAAT/i, the Theta-class and Nu-class shuttles (though I think there's a solid argument for these in medium instead), the T-6 Shuttle (turreted version with Jedi crew upgrades, though I think it's normal orientation will cause a problem), and the GR-9 Rigger. I guess the LAAT/c could also be considered but it feels very unlikely compared to the LAAT/i. The Eta-class is either small or medium. It's no longer than a Sheathipede but the wingspans might be enough to bring it into medium. Havoc Marauder is still possible in large but unless we see more of this shuttle in the renewed season, then I doubt we'll see it in XWTMG2. The NTB-625/630 seems even less likelier the more I consider it.