This page indicates that the numbers are the X and Y dimensions of the cap package.
By moving the cursor over the footprint I can see that the 6.3 appears to be the diameter of the can. I can’t see what the 3.9 relates to. It doesn’t seem to be the Y dimension. What is it?
It is the height of the can.
Although the size of the 6.3mm footprints is (nearly) the same, they have different 3D models attached for the different heights.
Here I’ve put a few in the foreground, from 3mm to 9.9mm (all 6.3mm diameter).