Whats wrong with choosing/qualifying 2 maybe even 3 boards from different manufacturers, and writing a little extra code to detect which one your software is running on and adjust things accordingly? Abstract the hardware interaction away from the application so that it stays as generic as possible and just need some functions to support the different platforms?
If youre not going to standardise on something, then you need accept the fate of building a more complex product in one way or another (hardware/BOM, software, etc).
Personally I'd probably choose the software route. Adding a microcontroller or some other device, which will need its own code written and maintained (and may need updating in the field), just to avoid writing some other code in your main application seems silly to me. And then you have two code bases potentially using two different sets of tools and toolchains, extra manufacturing steps, ....