The GUI window setup and positions are not linked to a specific model, so are not saved within the SKP file (template or not.)
Secondly if you start forcing options upon users, they will fight back.
Thirdly, the “Default Tray” is not intended to ever be the way that users use the GUI. It is expected that they’ll customize their GUI layout, by making more trays, etc.
I myself have already set up the trays the way I like them, with a tabbed array and the Layers and Scenes panels on a “Organize” tray.
This thread is about giving users more options, not forcing your choice upon them !