What you're looking for is a tool that allows you to adjust scale in terms of height and width, a way to tint preselected areas different colours, along with an intensity adjuster and possibly something to handle the textures, and for the models in elemental to be segmented so you can swap one piece of armour for a different piece of armour and mix and match.
That gives a *lot* of flexibility, maximizes the bang for the buck of each individual art asset (since it can be employed in a dozen ways instead of just one. If you have just one snake model, but you can adjust the size and tint it, it means your "one snake" just became "all snakes."
And means that your quest writers can click up a new special creature/object/item that's visually unique in the campaign by pointing and clicking *without* having to drag one of the modellers and a concept artist away from their jobs.
The cool thing is that AFAIK stardock is already doing this with buildings, allowing you to create arranged tiles out of barrels and other materials, and we know they're tintable. We also know there's a lot of flexibility in what your sovereign and individual units can look like, so it's not too much of a stretch to imagine they might go the extra mile and throw in x,y,z scale adjusters and a few more tinting scales. Combined with clever segmentation of the model pieces, and a good base library of assets, and you could do anything from making an iron golem to making a winged angel for your mod.