Probably charge you more to have it removed; that's not a standard option.I was actually thinking of removing the back seat and installing a small box with a padded top in its place for tool/emergency kit storage. That should significantly improve the amount of cargo space at the cost of a bit less comfortable ride for a passenger that will almost never actually be there (if I expect to have a passenger, I'll use my other vehicle).
I wonder how much they'd knock off the price with a rear seat delete option? I would probably trade that for cruise control or some appearance upgrades.
If not more, they might take it out after being built, but not give you any credit for it.
Might as well keep it and do the mod yourself.