jumanji, I'm going to explain the process, at least on all the many systems I deal with. Take a moment to read through, and if you want to stop deabting it and ask questions, do so and we'll continue.
1. You run the utility in Windows, which loads or downloads the BIOS file. It is loaded into a storage area on the motherboard. This is usually done after a version and compatibility check is done. You are then prompted to reboot.
2. Upon reboot, your motherboard takes over and goes into it's own processes of taking the file and updating the actual BIOS on the board. You see a 'DOS-like" screen, meaning it is plain text on a black background. This is not Windows, not DOS, and not any other OS. It's the board itself. You will see the progress, along with a confirmation message.
3. The system then reboots again, going through the CMOS process as normal, and then on to Windows again and back to normal. Some apps will reappear in Windows to give you a final confirmation and summary.
Once again I'm left with one unanswered question. What part of that makes you think it is more risky? If you had the BIOS on a flash drive and used a board's own internal hot key upon boot...the process of the actual flashing would be identical. If you created a DOS boot disc, well, now you are running another OS, like Windows, that is outside the control of the board, relying on another executable file, to flash the BIOS.
That's the frustrating part about this. You claim to only want answers, but you are skipping right over them. All we're trying to do is explain the process and why there's nothing to fear (nothing extra to fear over any other BIOS flash method).
To address one more of your points, if the Windows utility loaded the new BIOS, flashed the new BIOS, and didn't prompt for a restart...that could be worrisome. However, despite what you contend, that isn't how it's done in reality.
As for your last point...there is no flashing done from within Windows. You ask which is safer, Windows or DOS, yet you fail to see that you aren't even comparing apples to apples. The Windows utilities load the file so the board itself can handle the update. The DOS method still requires an OS and an executable file to handle the process....there very same thing you are so fearful of in Windows.