From the BIKI on execVM:
The Script is first searched for in the mission folder, then in the campaign scripts folder and finally in the global scripts folder.
I haven't tried this but I think the global scripts folder is referring to your Addons folder. So any script that is within a .pbo that is loaded could be executed. I assume that includes ones you load via modfolders. There might be a way to predefine functions linking to a script in a specific location, but I think the usual way would to treat the pbo as a folder. So a script.sqf inside myscripts.pbo would be called by execVM "myscripts\script.sqf";
Sorry for sound so vague, but I've never had to try it.