There are a number of workflows that use a tool of some sort to bake the mesh to a single material as part of exporting for the engine. There’s a variety of tools and paths to make this happen automatically, or semi-automatically – which one works for you (if any) depends on your specific tools and needs.
Then again, if you want to support team decals and individual unit damage, you may end up with some solution that requires multiple materials anyway for technical reasons.
In general, I’d expect CPU and pathfinding and simulation to be a harder cap on unit count in an RTS, than the difference between 1 and 2 material (instances) per unit mesh.
Also, if your meshes support articulation (aiming cannons or whatnot) then each mesh piece has a cost, in addition to each additional material.
If you’re targeting mass market Android phones, it’s probably best to bite the bullet and bake everything to a single material slot. If you’re targeting PC with add-in graphics cards, perhaps the incentive to do so is less direct. And if you’re an alone creator, do whatever it takes to ship the game ahead of any other particular criteria. “Shipping one game” vs “being too locked up in all the technical mintuae and shipping zero games” is a much bigger difference than “shipping a game that runs well on a GeForce GTX 970” versus “shipping a game that runs well on an Intel Iris 600.”