Is there any disadvantage with separate boards on the same frame having different sizes markers on them compared to the markers on the other board?
“detection” of markers first means you get screen space (2D) coordinates of the corners of a marker (and also its ID). detection doesn’t care what size each marker is.
in a second step, you know the marker’s expected physical size, and given that size, you calculate its position (distance) in space. either all markers are the same size or you have a table of marker IDs and their individual sizes
so no, it doesn’t matter.