They are both firmware, and both 'bios' (at least speaking loosely), and both EFI.
When we have taken risks, does not mean that we should take them as much as possible.If you've already burnt your MacPro firmware, when upgrading from 4,1 to 5,1, or after boot rom cleaning service from @tsialex, then why not do the same again? You also get the advantage that very many different GPUs will all work for the native firmware UI (incl. native boot picker) from then on. But if you prefer to burn it to the GPU (and if it's not an AMD with too little space), then go ahead - it's your machine.
That's why they are called risks. Every time is a risk.
But you do have a point here: if planning to use multiple GPUs, value of them might easilyexceed the value of cMP's motherboard.
It seems that even here in EU, professionals and companies are getting rid of their mp5,1s more and more. So it is now easier and cheaper to get a replacement.