I believe this can be addressed by rearranging the parts definitions, splitting them into multiple files and updating the references in the unit definitions. Others are using this method as a workaround for unit mods which exceed this new limitation on references per slot (seems to be 5 entries). This mod is much wider in scale obviously, and would require a substantial amount of work to vanilla definition files (more tedious than difficult), so it might be wise to see what comes up in the next beta patch. I should be able to test this over the upcoming holiday, give some feedback and upload some fixed definitions to inspect.
Briefly, you'd take something like this 18 variant_mesh parts list for persian tunics and separate it.
persian_tunics.variantmeshdefinition
If you scroll down to the 3rd and 4th tunic variant_mesh entries, at the end of those lines I've highlighted the mask switches. Those take the values from the faction rgb sets and swap their placement on the color map. If the mask switch doesn't appear for a model entry, it utilizes the default scheme (mask0=0, mask1=1, mask2=2). Since this giant list is being effectively truncated after the 5th entry, we're not getting to see any variants where the primary color (mask0) is alternated. Thus, the sea of orange in your screenshots for Persian Archers (along with scant model/texture variation).
To get around that, we'd split the parts definitions into multiple files of no more than 5 VARIANT_MESH model definitions. With this particular file, the tunic entries also have 6 slots each for trousers, so you'd either have to sacrifice one of them or perhaps come up with a more clever arrangement. Also, the method the game uses to determine the frequency with which a particular combination will appear involves the use of duplicate entries, so here too we'd need to give some thought as to how to split these definitions to achieve an acceptable result.
In any case, the other step would be to fix the references in the individual unit defintions to point correctly at the new data structure. Fortunately, there's even more wiggle room to be gained there at the higher level by replacing single 'top level' unit definitions with multiples. With a limit of 5 references per slot, I believe you could still get on the order of 125 variants per unit (say 5 basic variants containg references to 5 parts definition files per model part, each of 5 model definitions). That's obviously way more than necessary and also untested
As I said, that's not a trivial task, so let's see if the developers don't actually start doing something similar themselves (or otherwise increase the reference cap at higher settings). However, at least we appear to have options should this turn out to be a blind crusade to enforce some sort of memory budget. I really doubt they'd butcher their efforts in such a way, but then I think of how the FotS patch demolished the lighting in the base Shogun game for a lengthy period
credit to posters in
this thread for discussing the problem and potential solution