I happen to be helping a friend with a rather similar (But not identical) Gigabyte B450M DS3H WIFI, which has a Macronix MX25U12872F. He had the exact same issues about not being able to read/write and getting only FF FF.
After some datasheet reading, it seems than the MX25U12872F is cross compatible with the Winbond 25Q128JWSQ so most likely both would behave the same, at which point I noticed in the datasheet that both are hardwired to “Quad SPI” operation, which is what I suspect to be the true culprit.
Based on this post from other forum, the CH341A is not Quad SPI capable: CH341A Serial Memory Programmer Power Supply Fix - Page 3
Some further googling got me here:
https://www.downtowndougbrown.com/2021/12/upgrading-a-motherboards-bios-uefi-the-hard-way/
Which seems to make a CH341A mod for both 1.8V (Not needed he has the adapter) and Quad SPI.
So: Do anyone here with similar experiences can confirm if Flash EEPROM chips hardwired for Quad SPI need special support from CH341A and flashing Software? This seem to be a trend on Gigabyte AM4 boards.