Yes you get rear Hyd connection with the BH, and as others have said, don't need to load the rear tires with the BH, and no need to add rubber pads - they are so you don't tear up asphalt and you can bolt on a chunk of rubber tire tread your self.
As far as the seat - this would be a dealer question - he may have something available or be willing to swap them out for a nominal cost. There are aftermarket options too if you don't like the standard one.
The grappler - that could be the BH Thumb and a mechanical one is what you get with the
BH77 (a hyd one is very nice but $$$ 1000 or more. As far as a grapple, for the front those are nice but also $$$ and you need another valve and Hyd lines on the loader to use the grapple.
Since you are getting the QA bucket you might want to have the dealer add another set of remote hyd connectors on the loader at the bucket. This way you can add a grapple later (you can find them used).
The 2501 doesn't have a rubber deck and has the center hump - some options are stair tread rubber or anti slip, or modify a rubber car mat. I would live with it for a bit then decide.
Carl