You could also design the machine to rotate the channel 180 degrees, as to save money on an extra plasma.
Will the plasma's 5 degree bevel be an issue on the flanges?
Depending on the amperage and duty cycle of your plasma, that will determine your efficiency, I would think. You would have to spend a lot of money to buy two machines with the duty cycle and sufficient power to cut 3/8 all day long.
I am guessing you're looking at 120 feet of material a day. A larger machine (minimum 50-60 amps) should cut anywhere from 35"/min to 50"/min (possibly more +- 10%) so 1440 inches a day / 36" min = 40 minutes of cutting time per day. This is if you are running 2 plasma machines simultaneously. With one plasma, double that time.
In other words, theoretically, you are looking at cutting one 3' piece per minute if you are using dual plasmas. Total cutting time will be in the 1 hour range per day, if you run 7 days a week with dual plasma.
Figure in downtime for consumable replacement, stock loading and unloading, cleanup, etc. Don't know if you load these channels in full sticks, 3' pieces, use a forklift, etc. That is another matter.
Consumable efficiency varies with each machine, but the best IMO is Hypertherm. Electrodes last longer but cost a little more than the competition.
I might be completely wrong about all this, if I am I apologize. I know larger production or industrial plasma's can cut faster (such as High Def plasma) but you will break the bank on one that big.
It all boils down to what my racer buddies all tell me. " Speed costs money. How fast do you want to go?"