I think we already answered this.
If you have any User Event Script deployed on Sales Order, be it Before Submit or After Submit, it will surely fire on nlapiSubmitRecord( doesn't matter if you fire this in a Scheduled Script or elsewhere.)
A simple way to test this is that create a Before Submit User Event on SO and just write one line of code nlapiLogExecution('Debug', 'Test', 'John Doe'); and in the browser console itself just load and submit any record.
The Log will be generated as written in the script.