Re: Given that...
Microcode is specific to the CPU, it doesn't affect the motherboard. If the Microcode is added to the BIOS it is installed immediately on system startup, whilst if it's included in an OS the OS needs to start booting before the microcode may be installed.
This isn't anything particularly new, and OS already upload manufacturer firmware blobs into devices (network cards, graphic cards, etc) in order to make them operate, even with free OS (the drivers may be both cost free and open source, but the firmware often remains closed.)