Hi Everyone,
Well I think is "just" took me about 2 years to nail this script, so I thought it was time to share with you all.
I have created an script that based on floor markers and side markers, fully automatically created a correct bounding box, so you can easily cut out floor and have correct orientation for games engines like unity / mixamo.
Here the instructions and download to the script and floormat design:
http://www.pi3dscan.com/index.php/instructions/item/agisoft-how-to-process-a-scan-with-projection