Intel exited the Desktop Boards business soon after the release of the 8 Series boards. Once the standard (3 year) warranty period was over, the support team was disbanded and all maintenance work on the BIOS was terminated. The update that you recently saw released was put together by an emergency response team as a result of some serious security issues being found in the Intel Management Engine (ME) firmware. No other parts of the firmware package (BIOS or otherwise) were updated in this process. Unfortunately, due to the business exit, no other type of issue will be considered just-cause to receive similar attention. Do not expect these issues that you are seeing to be fixed in the future; they will not.
It is certainly in the realm of possibility that the problems that you are seeing were introduced after the original production BIOS was released (i.e. were bug(s) introduced in some subsequent BIOS update(s)). Unfortunately, whether you will be able to back your way through these updates (and possibly locate one that doesn't exhibit the issue(s)) is going to be limited by the ME firmware. It simply may not allow you to go back beyond a certain point. If this is the case, you will have to stick with what workarounds you have in place.
My only suggestion is for you to investigate whether the use of (or disabling of, as the case may be) UEFI support makes a difference in boot order handling.
Hope this helps,