I believe non-revs flying for official purposes (i.e. positioning crew) get preferential treatment WRT overhead bin space, since they need their crew manuals on their assigned working flights and are not supposed to check them.

UA has started rolling out mobile bag-tag generators for the gate agents, so if you have to gate check a bag you get a proper barcoded bag tag just like if you'd checked it at the check-in desk. I could imagine some bags being barcoded and not turning up in the cargo hold could cause issues but I'll have to ask my GA friend next time I see him. Short advice though would be it's probably far less of an issue with the yellow paper tags than with anything computer tracked. FWIW UA is starting that because apparently the yellow tagged bags make up a huge percentage of the bags that arrive late or get lost, and getting the barcodes on them will hopefully lead to better tracking and more consistent routing.