Short answer: no. But I did stumble upon some other interesting interactions with Devour and Devour Cargo Hold that might help find a working solution.
I checked out the Devour Cargo Hold and saw what you meant. So I started messing around with it but couldn't make it work like you wanted. I initially thought it was hardcoded so that when you load an enemy unit, it disables manual unloading.
However if you remove "Enemies" from the target types of both Devour and Devour Cargo Hold, you can load almost any unit, ally or enemy. That's right, you can load and unload enemy units whenever you want! The catch? The "left-click unloaded" functionality works as per normal, so unfortunately this doesn't help your case here. For those wondering however, the only units that can't be loaded are flying units and structures and this seems to be hardcoded. Another oddity is that if you add one of the Unload abilities along with the default Devour and Devour Cargo Hold, you can unload the enemy unit with the ability but it will still disable the manual left-click unloading.
So apparently Devour disables the manual unloading by default but I couldn't figure out what causes it. In the end, you might have to trigger your transport system unless someone else can find a proper solution to this.