When I flew Air Canada last May, I had a confirmed reservation for my bikes, but I did it after I booked my tickets.

I agree with you that regional jets are dicey with cargo, not to mention if they fill up luggage sometimes has to wait for an empty plane (the college I went to was serviced by one CRJ and two Saabs a day, and at break time some friends would inevitably have to wait for the return of their luggage). Even if it costs you a reservation fee, have you considered booking over the phone, and getting a confirmed reservation for your bikes at the time of purchase?