Looking for a good cover that is trailer-able.  Most covers say don't use while trailering the vehicle.  I'm also concerned with the fabric flapping and causing scratches to my windshield.  Any suggestions?

Reason I ask is that I wanted to take the Z800 on a trip but I would be going through heavy rain and didn't want it to get soaked.  Plus I load mine backwards in the truckbed so I can center the weight over the axle because I pull a camper behind the truck, too.

[2015 Z Force 800 53/Trail EPS]

Sorry, no soft cover is recommended to use while transporting for that very reason. Maybe build some sort of partial enclosure on the truck to deflect most of it or some type of hoop frame from the bed that you can tarp over it with. 

...I load mine backwards in the truckbed so I can center the weight over the axle...

JFI, there's a commercial truck scale near my home that closes but leaves their display active. I tested with my 800 Trail in my shortbox Ram, loading it first front axle ahead and then loaded again reversed.  To my surprize there's only >20 KG difference truck rear axle weight!
I'll have to take the SXS there and offload it, and measure the machine's actual front/rear weight, but in the truck bed there's not much difference resulting from which way you load it.