I wonder if a possible solution could be that instead of using the logo, we create an image within a rectangle format using the site logo & the header background color the site currently uses.
We would need to do this on the backend, but using an image block with the included color as the background would prevent gmail from inverting the color of the background.
For what it’s worth, I tested out multiple large brand emails in my gmail app while set on dark mode, and the majority of them have not solved for this either.