Or should I convert all modules with functions that are not using rest path to main modules so I can declare the output option?
Well, similar to that (I hope I got you right)... You can convert all of your modules, which include RESTXQ annotations, to main modules. A main module needs to end with a valid XQuery expression, which can e.g. be an empty sequence ().
It’s true that main modules can’t be imported from other modules. In our own projects, RESTXQ modules basically serve as entry points, and most of the application logic is stored in other modules (which we store in the repository).