If you purchase an extra seat for comfort, the extra seat has all the same benefits as another passenger would (checked bag allowance, mileage accrual, VDB compensation etc). I don't see why you couldn't earn miles with a 2nd carrier on the 2nd ticket.
And GA's do scan both BP's if a person has bought 2 seats. You'll have a BP that says Smith/John and one that says Smith/Extra Seat or something like that, with two separate ETickets.