Your latest version seems to have a bug wherein the add header image function doesn’t work properly and conflicts with WordPress. If I want to have a header image, I have to simply do it via WordPress header functions.
The header image is a built-in WordPress function which Mantra supports and uses. There’s no conflict there.
You are confusing the header image with the logo. They are two separate things, you can use either, both, or none.
Just don’t try to upload your header image as a logo, it will not look right.