Whatever rocks your boat and can allow the necessary tool to work.
BIOS upgrades in general sucks, some more than others.
Some archive apps like WinRAR can extract files from self-extracting EXE files. Also look around for other softwares that can do this.
In some cases a command line option will allow the EXE to be extracted but not installed - but you have to do some digging.
Of course - the above is provided that you have at least one Windows machine around.
Also check around on the Motherboard manufacturer site - sometimes they offer both an EXE and a ZIP archive, and if nothing else contact their support. If nobody pesters them about the problem then they don't care.
And finally - also look at Tyan and Supermicro for motherboard, even though their target is server motherboards they may have some suitable motherboards for you.
WinRar do have quite some ability to actually extract info from EXE-archives, so do Winzip and 7-zip. (not always though)
Also search the sites for the manufacturers to see if there are unbundled BIOS copies - and contact the support of the motherboard manufacturer telling them about the problems it causes you.
Also look at Tyan.
That may vary on which model. Some years ago a friend of mine went through a whole box of WD disks in a year on a single machine.
Even though it's not computer nerd stuff it's geology nerd stuff - and it might impact the rest of us so I did approve of this.
There have been way too little competition in this area the last decades. Considering that the Russian RD-180 engines designed in the 70's&80's are still seen as state of the art it is obviously a stagnant situation.
You must realize that the computer has it in for you. The irrefutable proof of this is that the computer always does what you tell it to do.