I do not have a seat bag while running the trunk. Those items are stashed in my rack trunk. 2 tubes, tire levers, multi tool, patch kit, and a few misc items actually do not take up much space in the trunk and are easily compressible. I swap between my seat bag and the rack trunk on the weekends or when I am not using it. I guess that could be annoying but it does not bother me.
If that is annoying one could always run 1 or 2 panniers.

I am not sure about bringing bikes in the store. They do not mind for service but to see if something fits.... I would be inclined to say they wouldn't mind but I would ask first.

As for prices, performance is cheap. Bicycle Village is mid priced. Golden Bear is a bit more but has great service but that is what matters most to me.