How are you compressing the rear suspension when it is on the centrestand? Front wheel in the air? That seems dodgy. Are you thinking track stand?
I've never used the centrestand when trailering, but if you tie down from the passenger foot pegs, the rear suspension would be compressed. Rear tire would be up in the air if the front forks are cranked down harder.
But re-thinking about it, it's probably better to have the rubber of both the front and rear tire on the floor of the trailer so it doesn't slide around laterally when turning or going over bumps.