Could you elaborate on the problem you hit with pinmux spreadsheet?
I would suggest using pinmux spreasheet to generate both pinmux/gpio dtsi instead updating them manually in case you missed something.
Could you get a scope to check?
I would also suggest you apply the following patch before verification.
40hdr - SPI1 gpio padctl register bit[10] effect by gpiod tools in JP6 - #20 by KevinFFF