Is it possible to change the new script path of the PythonScript Plugin away from Users\Appdata ?
Not currently, other than creating a portable version of N++ (create a doLocalConf.xml), then it will default to Notepad++\plugins\config\PythonScript
You can manually add scripts to the config file from any path. The file is reloaded when the config dialog is opened, so you can comfortably edit the file in N++. See PythonScriptStartup.cnf. The format is a bit odd, but it's obvious - just put ITEM/c:\path\to\your\script.py
Other than that, what's your use case?