If those are the limitations of the third party software, those are the limitations of the software. I can only recommend alternatives and work arounds through our own software packages. If the issue you are experiencing is with MS One Note, then that is an issue you are going to need to speak with a technical representative from MS about.
There is no way to lock in defaults on the printer for scanning, that is all done through the software would use on your system.
I apologize for the inconvenience that this might cause you, but I hope you are able to find a resolution.
-Spencer
PS if you do find a resolution post it back up here, and I will be sure that gets out to anyone else who might experience the same issue. Have a great day!