Order of Group Clones, Group Mattes, and Group Linked Adjustment Layers
Order of Group Elements
The order of Group Clones, Group Mattes, and Group Linked Adjustment Layers is not customizable. Going from the top-most layer, it is always:
Group Linked Adjustment Layer
This is because a Group Matte and/or Group Linked Adjustment Layer will have the same effect on top of the Group Clone as them being contained in there, so most of the time there is no reason for the order to be different, and the performance and layer/effect clarity is improved that way since matte layers and adjustment layer effects don't have to be copied to all group layers. (If you still want to change the order of these group elements, there is a way.)
If you move the group elements around and execute Refresh Connections on one of them, they will be reordered in the order described above.
Changing the Order of Group Elements
Group Linked Adjustent Layer and Group Matte contained in a Group Clone
There are a few situations when you want the Group Matte and/or Group Linked Adjustment Layer to be contained the Group Clone. (If you want to reference a Group Clone by an effect, for example, and you want the matte to be baked into the clone already.) The solution to this is as follows:
Since sub-groups can contain their own Group Clones, Group Mattes, and/or Group Linked Adjustment Layers, you can create a sub-group that holds a Group Linked Adjustment Layer and/or Group Matte while the higher group holds a Group Clone.