When I lived at Houston I was IAH based EXP for two years.
1. I do not think I always got cheaper fare. It was give and take, some time CO/UA had cheaper fare which got me faster because of non-stop to the destination. Then I still remember one of the business trip where I had to go to MSP. I saved company +$500 by flying AA IAH-DFW-LGA-MSP than flying CO/UA non-stop IAH-MSP.
2. No, non-hub city did not provide any better upgrade opportunity, Actually DFW-IAH was very elite heavy route with international passenger connecting at DFW heading to the Energy capital of the U.S. I do remember the first flight of the year where I did not get an upgrade was IAH-DFW.
By based out of non-hub city I found that agents went out of their way to accommodate my situation. On one of the trip DFW was all messed up due to heavy weather in the area. I got an e-mail notice that my IAH-DFW flight out of 11 a.m. was cancelled and rebooked onto afternoon flight. That did not work for me, getting on 9 a.m. flight would have worked but trying to call AA was long wait due to massive cancellation/delay at DFW. I just headed out to the airport, got in time for 9 a.m. flight. I asked an agent at check-in/ticketing for 9 a.m. flight even though I was rebooked on an afternoon flight. The agent first told me 9 a.m. flight was booked solid and it was even oversold. After looking up my reservation the agent said let me talk to revenue management to see if they will force you into 9 a.m. flight because you are EXP. After little bit of wait and doing some typing, the agent printed out a boarding pass for first class. Not just I was confirmed on oversold flight, but gave me an upgrade. I thought that would never happened at DFW or ORD..