It's not "supported", but I see no reason why it couldn't work. You'd probably want to do it from the ResourceLoaderRegisterModules hook (which is fired after core modules are registered). Also, $moduleInfos is protected (because you're not supposed to modify it :D), so you'd have to cheat with some reflection to access it probably.
But perhaps there's a simpler way? What are you trying to do? The simplest thing would be to just create your module, give it 'position'=>'top' to make it execute before almost all other modules load, and add it on all pages from some hook.