No Hard drive recognized when starting from disc.
I do not use "Mattozan", games or VR software (I only use my PC for work/code writing). But if the Mattozan software specifies that you should flash from "within" windows environment, and leaves no room or reason for you to assume otherwise, there may be a good reason for that. Modern flash BIOS can be updated "live" from within the OS. This allows other active OS processes to be utilized, which cannot be accessed from a boot floppy/CD made specifically for flashing BIOS.
However, that being said, my personal preference is to use the boot floppy/CD method for flashing BIOS, because the OS may be contaminated by a virus, that can permanently damage your PC if this is the case, when you update.
Thus, you have two choices; take a risk, and follow Mattozan advice. But I would strongly urge a VERY thorough virus scan, including RAM and MBR, before doing this.
The ONLY safe option is to flash your BIOS with an update supplied DIRECTLY from your BIOS or mfg/motherboard web site, which has some signature or encryption verification (to assure it is authentic, not supplied by some 13 year old Chinese or Russian hackers who hijacked the website), and then, to apply the update from the floppy/CD booter. This completely bypasses your OS, so if the OS is damaged, the BIOS will still be correctly updated.
Thereafter, the Mattozan software, if it is legitimate and well written with safety as a consideration, should recognize the update and proceed normally. One exception might be if the BIOS is newer than the Mattozan software version (in which case you may need a Mattozan update as well).
Perhaps you can post the exact wording of the message/READ-ME for the software, and I can better advise you if there are other considerations to weigh?