I was looking at the stock Bonnie seat as well as aftermarket to replace my stock Scrambler seat. I ended up buying a used Mototwin seat and found out it was about an inch shorter than the stock Scrambler seat - the gap shows up up front - you have about a 1/2-1 inch gap between the front of the seat and the tank. Not sure if it is the same with the stock Bonnie seat but I would guess it is. I will measure my stock Scrambler seat and let you know. Otherwise the fitting tabs match up. I also think the height is the same. Again, I can measure and let you know.
As far as comfort, I can't see the stock Scrambler seat being any more/less comfortable than the Bonnie. Both don't have much padding or shape. I will probably take my stock Scrambler seat and have it re-shaped and re-padded by Sargent. They have done seats for me in the past and I was always very happy with the results. I like the looks of the Mototwin that I have and may just copy that with more height and some additional padding and shape.
As far as comfort, I can't see the stock Scrambler seat being any more/less comfortable than the Bonnie. Both don't have much padding or shape. I will probably take my stock Scrambler seat and have it re-shaped and re-padded by Sargent. They have done seats for me in the past and I was always very happy with the results. I like the looks of the Mototwin that I have and may just copy that with more height and some additional padding and shape.