I just tried to create this problem on my local machine with folder sites and related sites mode but it seems to work correctly for me. I add the setting and now site 2 uses /Data/Sites/1 as the starting folder for files. Using the browse button for a link when I expand the "Pages" node it correctly shows the pages for site 2 not site 1.
So I am not able to validate this as a bug. If it showed the pages for the wrong site I would consider that a bug, but for me it shows the correct pages (though I am testing with the latest code so possibly it was a bug that is already fixed but I do not remember ever seeing this bug).