Scripter is a "live" plugin that sits between the MIDI region/input and the software instrument in the signal chain.
To record the output of scripter (and the script you are using) to a MIDI region please refer to the second part of this article.(starting at "Use the Mac’s IAC Driver to Capture MIDI" - ignore that it is refering to Arpeggiator - it works for all MIDI effects.)
Alternative for capturing the midi: http://www.audiocr.com/midi-fx-freeze/
1. Create a software instrument.
2. Choose scripter from the MIDI FX plugin dropdownmenu.
3. Paste the contents of the downloaded script (and replace any existing code) into the script editor window of scripter and press 'run script'.
3. Alt. If you received an installer (ex. Chordio.pkg) you can skip this step and just select your script from the presets in Scripter (in the factory presets in a folder called 1. LogicScripts).