Keep in mind, the reason the Imperial factions all have different rosters is
not because each faction only used certain ships, nor is is that each ship type was only available to certain factions. They all would have been present to some extent in each Warlord's force. The reason they have different build options in the mod is because there's enough units under the "Imperial" umbrella to do so, which there'd be absolutely no reason to have under the same faction (which is why we didn't just piule them all into one group), and because, crucially, it's only worth it for us to do the Warlords individually if there's something different about playing them all. For example, the PA's fighter focus- that's
not because the PA was canonically set up that way, it was simply a different way to express the Imperial military doctrine, while still keeping it Imperial. We also tried to make it make sense in certain ways, ie PA was in the Outer Rim at Endor, so since we were dividing it anyways, we stuck with giving them some of the stuff typical of the Outer Rim when the Empire fell. Later on, as the post-Endor period progressed and the PA became the main territory in the Remnant, that wouldn't necessarily have been the case. It's a gameplay decision, not a lore one.
By starting to mix them all again, leaving aside overfilling the build bar with redundant units, you're basically removing the point of us putting in the work to make those extra units in the first place. We could just as reasonably have made every single Warlord roster identical except for the one or two unique things different groups did have (Raptors for Zsinj, Enforcers for PA), which puts us back to square one. So, we don't need to edit the rosters to show they all grouped back up because, again, those rosters are a gameplay distinction, not a lore-based one, and the more you try to mix it up, there's more and more reason not to have it in the first place. You just end up with a ton of redundancy.
the IR is a rag-tag group, the pulled together groups of almost every remnant of the empire
Just for emphasis, from a lore perspective, this wouldn't have impacted the force composition of the Remnant at all- they weren't a ragtag mix of fleets that had different in-universe compositions, they were still the Imperials, with the same set of Imperial ships. It's only a rag-tag group if you're taking the premise that each Warlord group had a distinct set of ships they used, which, again, is a gameplay mechanic in the mod to help justify their existence, not really something that exists for lore purposes.
and, no, not as buildable units. my logic, after reading Darksaber, is approximately 50-60 of the Crimson ships survived the United Warlords Fleet campaign. they didn't all immediately disappear. if we go by the 15% of forces, that is still 7-9 CCVSDs left. could we see decreasing numbers of them in the later GCs, like 8 in orinda, 5-6 in final push, and 4ish for Caamas Crisis?
After the first battle with them, at Harrsk's fortress, before any campaigns they were used in, there were 62 left. They then supplemented them with the regular grey ones, after which we have five confirmed killed, including 13X, so we have at most 61 and at least 57.
And keep in mind, again, how insignificant the number of Katana Dreadnaughts and Crimson Command VSDs is in the context of the broader Imperial fleet. That is a very small number of ships. They're available in their respective parts of the timelines because they're important to the plot or because of who was associated with them- earlier on Crimson Command is important because it was the core of Teradoc's fleet, then it was one of the first things Daala got from the Warlords, and was under the direct command of her main deputies. They were part of the main fighting at that point, which is how they lost 10-20% that we know of in just the "on screen" portion of their first year, including the flagship of the fleet. After that, they're not super prominent in the fleet. It may make sense to have one or two as starting forces in Orinda as the campaign set right after Daala resigns as a historical curiosity, but keep in mind the jump between even Orinda, which wasn't a thing at all in 2.1, and the next GC the Empire's present for is 6
years. In Art of War, you've always kept whatever you had, but in 2.1 single-era GCs, that is a huge jump, during which time who knows how many of the ships were destroyed. They certainly were no longer central to the fleet.
The bottom line is, the way we have to (really, the only way we
can) differentiate the eras and the Imperial factions is trying to emphasize what was important or even just a peculiarity of any group at any given time. Did later successor groups to Daala and Thrawn probably have CC VSDs and Katanas floating around? Probably somewhere, but not the same number, and they weren't made as central to their command structure and operations, so it removes some of the qualities of each of those leaders/eras. You can probably make the case for any given group to have any given ship at any point, and not technically be wrong- the big exception there being some of Shadow Hand's toys, but we have 5 playable Imperial factions, one of which has to be split between 5 eras itself. Secutors, Procursators, Praetors, these were all probably things even Pellaeon (or insert other name here) had at least one or two of sitting around, but probably fewer than other groups were likely to have, and more "mainstream" stuff was likely the bigger focus of his production, which is why we split stuff up the way we have. When the only reason those ships exist in the mod in the first place is for diversity (there wouldn't be a unique game role, and therefore there wouldn't be a justification for us to include them otherwise) we have to be a bit more discriminating, otherwise, yes, every faction could have every ship and it would probably be more lore friendly because all Imperials had a huge selection of ships.