Why wouldn't it be a nice thing to do? It's easy to uninstall the old version, update windows and reboot, then install the new version = problem fixed. What's not nice there?
FlashSPI is a DOS program, you have to boot to DOS, it has nothing to do with your system being x64, it wont work in 32 bit system either, you must boot to DOS via floppy, CD/DVD, or USB.
If you are going to use @BIOS ever, download the file you want manually, and then use the update from file option, do not download from online server because sometimes it will say no BIOS, or grab the wrong file (Yes, these are problems with the program so you are correct there - just more reasons we suggest not using it)