You can absolutely call full programs from inside the Main program using the Subprog command. Not exactly sure what about that isn’t meeting your needs. Otherwise, yes you TECHNICALLY can’t call a subprogram from within a subprogram. You CAN workaround this though. See my reply here:
In that example, the subprograms I inserted were VERY basic, consisting of only a popup, but they could very easily have been a fully fledged program, complete with waypoints. You CALL the program with a Script command, but you’re still free to edit waypoints like normal on the sub program itself