The Problem is here, that if you change the copper layer, the according technical layers do not change. This could lead for example to SMT pads on the bottom side, which are coverd with solder mask. That shoud be avoided in it's root.
In the first 3 sets, the layers can not be changed by the user, this is, that he get not confuesd by automatic cahanging checkboxes, which, her perhaps has changed manually before.