If I understand you right the system beeps directly when starting up and not after finished POST when starting up windows. You can’t access bios settings in this beeping state?
Then this is firmware related and a clean windows install hasn’t anything to do with it.
I’d strongly recommend a complete backup of the complete firmware! Might be ME 16, then tools would be linked here:
fptw64 -d spi.bin
Otherwise you could try to load the bios default values, that might overwrite the SaSetup.
If that doesn’t work and you got the same output than the TO when changing the variables, you might try revert the value to 0x00
In addition in the original thread there’s a mentioning of beeping error with another solution.