I largely agree with you. It's down to who is paying for the service. Is the original business being given the choice and offered the chance to make the route open? Increasingly operators are just throwing a price on a contract and running as per the original script and don't even try to say 'have you considered doing things this way'. An interesting connection that I have picked up on too is that where Amazon seem to deal direct with the bus operators, that routes are open to the public, but as soon as it goes through a 'travel solutions' company/broker, then it becomes closed door. This strongly suggests to me that Amazon don't mind the services being open, and that it's just because of the middlemen why the services become closed door. How many businesses, if they were given the choice and the pros/cons (to make an informed decision. Ie the route can claim BSOG, but you will lose some of the flexibility), would instead choose open door? I know Zeelo and First Travel Solutions etc just point blank won't offer these options to businesses.
Of course without specifics (which I appreciate you are unlikely to share), it would be hard for my to confirm your thoughts. There can often be strange flows that pop up though on these sorts of routes. Speaking to other commercial management/staff, they have been surprised that similar workers routes have ended up with some very dedicated, regular passengers who aren't/weren't using the services for the purpose of travelling to the main workplace for which the service was intended. The upset with Ensign & Hornsby too when their routes went closed door, similarly says that there was demand for trips despite them being strange routes.
It's easy to just say 'the service would be useless', doesn't mean it's always right though.