Yes, its obvious the original seal has been removed and its been re sealed.
If the cosmetic condition is intact and the TV is operating fine, I would not stress about the state of the box. It could have been opened for a variety of reasons.
You have nothing to worry about. The TV has a warranty with Sony (I assume they honor online purchases from other websites). If anything is wrong, call them up to inspect, replace or fix it.
My X7500 did not come with any protective layer on the screen. It had the usual plastic cling film like covering on the plastic borders of the screen (as reported by others), over the brand name and over the top ventilation covers at the back and right behind it. All the associated accessories such as stand, cables, were all intact and in their original packaging which is a sealed bag. There were no marks on the screw holes either which would generally indicate if it has been mounted on a wall mount.
Good choice on the TV make and model.