Good morning.
After spending quite sometime on the subject, I found out the reason for the RTX3090_V3.exe not update the VBIOS as originally intended.
1. Unpack the RTX3090_V3.exe with 7z (7-ZIP) and you shall find these files inside

2. Open the selected file "Testini.txt" and you shall encounter a cross-refence list of OLD/NEW BIOSes "names" not "number"
and this is the main reason for the exe being prevented from working properly.
3. If you go then to the website
https://www.techpowerup.com/vgabios/?manufacturer=Asus&model=RTX+3090 you can select your actual graphics card model
to see the refence on the text box for your BIOS "name" and "number"

4. From this I was able to reference which VBIOS from all the ROMs inside the RTX3090_V3.exe was the correct one for my RTX3090 Strix OC
- Performance
Version: 94.02.26.C0.16
OldVersion = 94.02.26.00.AS26
NewVersion = 94.02.42.00.AS46
- Quiet
Version: 94.02.26.C0.13
OldVersion = 94.02.26.00.AS27
NewVersion = 94.02.42.00.AS47
5. Then I used the very same nvflash which was packed in the executable to update both "performance" and "quiet" VBIOSes using elevated DOS command prompt
nvflash --protectoff [to allow BIOS change]
nvflash --save name_your_file.rom [to save current ROM]
nvflash -6 94.02.42.00.AS46.rom [Performance BIOS]
nvflash -6 94.02.42.00.AS47.rom [Quiet BIOS]
nvflash --protecton [to protect BIOS from being changed]
Everything you need is already inside the file ASUS provided...

I hope this would help.
Cheers!!