Let me answer with a question, how much are you willing to pay for how much output power side routing with computer control?
Adjacent channels "only" could be shunted by adding 3 high current SPST relays, but these would cost money. Take up space, and require some extra glue circuitry.
A more comprehensive output steering matrix might be provided with solid state switching but this could compromise path integrity (distortion, reliability), and again will cost more money.
The customer is always right, so how much is it worth to you to "automatically" jumper outputs together, to save the effort of connecting a few jumpers? Note: The cost of adding automatic output shunts will have to be paid by all customers, even those not combining amp stages.
Re: Avoiding input/output conflicts, I would expect amplifier outputs to not only tolerate transient short circuits to ground, but hopefully shorts to each other (when not linked). If they detect output current ( a useful feature) they could pretty quickly identify fault conditions to protect themselves. Of course do not take my speculation for fact. Caveat lector.
JR