I think this is a valid use case, but I am not sure it has to be solved the same way it is currently being done in Mobile.css.

Rather than coding a template specifically for the MobileFrontend extension, it seems more appropriate to code it for a skin (e.g. skin-minerva, per T197617), and/or for a particular viewport size (@media).

That would make the template more maintainable in long-term, and also benefit users more widely instead of being limited to MobileFrontend. If the style in question is for Minerva, it can all users of Minerva (including those that use it on tablet or desktops). If the style in question is for narrow viewports, it can benefit narrow windows in the Vector skin as well ("responsive design").

Should allow for "desktop-only" styles

Media queries can be utilized to give you "desktop-only" and "mobile-only" styles. They can be used like this (we use this exact same mechanism for the existing mobile site):

.desktop-only {
  display: none;
}

@media all and ( min-width: 1000px ) {
    .mobile-only {
      display: none;
    }
   .desktop-only {
      display: block;
   }
}