Both 'Private Sub Workbook_Open' And 'Auto Open' Run Sequentially

I have built a complex vba & multisheet spreadsheet that I am looking to secure against all the common attacks. So I have:A Workbook Open pw;
VBA password (29 symbols/numbers/Caps/lower case)
Very Hidden worksheets
Hidden rows/columns
Restricted scroll areas
Workbook protection
Code that auto protects all sheets upon opening
Registry referencing in Workbook Open with timed closure if not matched
Now I am on the last leg of implementing protection against Application.EnableEvents = False; force enabling of Macros and hiding of toolbars, scrollbars etc... Phew.

Soooo, in my research, I have learnt that if EnableEvents = False, Workbook_Open is essentially skipped and the security VBA routines are disabled. To get around, I have copied the entire contents of the Workbook_Open routine to a module under Auto_Open. The first line of both these scripts is: Application.EnableEvents = True.

Works! So far so good.
However, I have a Msgbox prompt in the scripts that displays twice. So in essence, Excel is running Workbook Open first, then Auto Open second.
If I open another instance of Excel and run Application.EnableEvents = False first before opening my spreadsheet, I only get one message. So only the Auto Open script runs.