They certainly can do this. I've interlined several times in the past with AI to AI, AI to *G, AI to other AI interline partners.
The only issue you could face is the competence of staff at a small airport. Since you haven't mentioned where you're coming in from. Even at a smaller airport, senior staff would be able to interline so ask firmly at check-in. Of course with a 5 hour layover you have plenty of time to recheck your baggage, balance your cheque book etc. before you can collect your BP from UA about 3-4 hours before departure.
You will not be allowed into the departure hall area of the airport till 4 hours prior to scheduled departure. Also you will not be able to do a eBP for UA - it will have to be a paper BP you collect from the UA check-in counter.