What is the exact type of your chip? As I mentioned that, the Flashrom identifing the chip as a "W" variant (W25Q64.W) what is a 1.8 V chip and the RPI header has a 3.3 V rail. If it is the 1.8 V variant chip, you need to buy a 3.3v to 1.8 V adapter (like this https://www.ebay.com/itm/1-8V-adapter-for-Iphone-or-motherboard-SPI-Flash-Memory-SOP8-DIP8-W25-MX25/152133479949?hash=item236bdcae0d:g:gQAAAOSwnNBXY9KL ) for your RPI SPI communication.