Will my encrypted Python script work on Linux and Windows Systems? Yes, it will.
Can I encrypt Python modules? Yes, you can. Python Function/Module files can be protected. For added protection, you can choose to allow importation of encrypted modules ONLY from other encrypted python scripts.
Can I encrypt my Python script AND use PyInstaller to convert it to an executable? Sure you can. But you shouldn't have to do that. Once a script is encrypted, pyinstaller is not necessary unless you wish to avoid requiring users of your script to have python installed on their systems.
Script File Size
Is there a limit on the size of Python scripts that can be obfuscated/protected? No, there is not.