In managed mode, the "set in file" column in the variables table, and variable history should no longer show the full path to the files, but only the path inside the layer. For example, instead of /home/user/_poky_master.toaster_cloned/meta/conf/bitbake.conf only meta/conf/bitbake.conf
Bug 7463 covers this *** This bug has been marked as a duplicate of bug 7463 ***
Verified as duplicate