No, I definitely do not agree with your suggestion. In addition to the comments made by @Ealfardan, which I do agree with, the term Reference has a specific meaning within Manager and the Liquid templating language used for display of transactions. It refers to the identification of the current transaction, whether that is a sales invoice, order, payslip, journal entry, etc.
You have exactly described @lubos’ Option 2, except that you want the custom field to be defined for you. In that case, you would lose the ability to name the field according to your usage.
@mauroskov, you actually do not need to do any update. Any content entered in the former free-text Order number field is preserved and displayed on completed forms. This was explained in the thread where this subject was originally introduced: Order number has disappeared from Sales Invoice - Edit screen - #2 by lubos.