Overlays not bound to core configureation

Is there a way to get the different overlays to save with each individual core selected? An example would be when I open Nestopia and load a ROM, I need to switch the overlay to the NES pad every time. Same with all other cores.

I am using the 2-7-2015 nightly for android. My phone (Note 2) is also not rooted which could be a related issue due to kitkat’s problem with writing to external SD cards.

One other thing I had noticed is I had tried pcsx-rearmed with Gran Turismo. I had switched the controller type to analog and selected the dual-shock overlay. The game worked fine, but when I brought up the Retroarch menu, none of the directional pads worked with the menu; requiring a force close on Retroarch to get out.