Thank you, keilmillerjr and raygun for the ideas. If I ever decide to publish my frontend I will sure adopt one of these approaches.
I already have 9 emulators with 2 alternates using a single, very adaptive, layout. Although there are some advantages to the keilmillerjr method, the apps I made to manage my setup are very dependent on the romlists and a duplicate emulator would complicate things a bit so I'll stick to the file approach for now. Will look into the ultrastick method, tho.
And I look forward to developments on your idea, raygun!
ps. This is my layout. The screens might seems similar but everything changes from one to another, from the font to the spacing and the way they display the overviews, for instance. (the two screens on the right are the alternate VB and Vectrex)