As a matter of fact, no, I did partition and format it on my Linux box. I did not think it would matter. I will try this though.
I wonder however, what the difference is when I let the Mega65 handle it? Does it add some "secret ingredient" to the filesystem, e.g. raise a special flag?
From the MEGA65 Welcome Guide (https://dansanderson.com/mega65/welcome/setting-up-microsd-card.html):
Preparing the microSD memory card
To use an SD card with the MEGA65, it must be formatted (erased and prepared) using the MEGA65. The SD card works like a regular storage drive when connected to your PC, but it contains additional data not visible to the PC that is used by MEGA65.