You can use a 45 degree mirror and shoot a panorama perpendicular
That's smart, I will remember that! (Easier to control the camera as well).
Looking at your action shot: My experience is that at that distance and angle you will have a slight blur from the depth of field at the top and bottom of the photo, even at f11. (If you go much higher than f11, your image quality will degrade because of diffraction). Shooting straight down will make for sharper images. The longer the lens, the more shallow the depth of field is (you can find depth of field calculators on the Internet or on your smartphone. The depth of field for a 200mm lens can be mere centimeters even with the subject far away), so using a 200mm might be harder than using a 100mm at closer range (or even 50mm). Normally the lens distortion of a wider lens would be a problem, but because you are using Photoscan this is not an issue.
Also, I can really recommend getting a wireless or wired shutter release to avoid moving the camera when pressing the shutter button (it might seem trivial, but if you want perfect pixel sharpness it's very important). Another option is the 2 sec self timer delay, but that is a bit slow to work with if you need to do many photos like this.
Be sure to disable Image Stabilization on your lens when you are using a tripod.
Another option would be to suspend the camera from the ceiling, and slide the prints on a table (if you want to make it really fancy, get some line lasers to show your exact field of view from the camera to make the positioning easier. It would be an easy step in between automated scanning and working on the floor
If you are only interested in the texture you can use the Sparse Cloud to generate the mesh. We have had good luck with that (you could align with more than the recommended 40k points to get a Sparse Cloud with more points if needed).