It was rather common for us to take freight cars to Cumbres between the locomotives. It saved a bunch of time switching at Cumbres, and if we had enough cars, we could highball Lobato. Way back when, we had an electric signal line through the train to a siren box in the road locomotive. Having freight cars on the head end would not allow it to be used as the freight cars did not have signal lines.
Running with the second engine cut back into the train is not much of a big deal. Operation is not that different. The road engine cannot pull more than it's share of the train, so the helper up front always has the slack pulled tight. Only issue would be an emergency stop in which the road engine must keep the throttle opened until the train stops to keep the slack stretched.
This method is actually easier on the old freight cars as there is only 1 locomotive's power going through the drawbars instead of 2 when both locomotives are on the point.