I don't agree. I've fit people using flat pedals, it requires more work and a critical eye so I imagine your shop doesn't want the hassle. Usually I ride with them outside, watch them climb a few hills and look at the bottom of their shoes - from this it's easy to figure out where they like their feet and go from there.

Anyway for your specific issue it could be a few things. The thing I see the most is a muscle imbalance, do you sit a lot - especially for your job? Do you do any stretching? How do you warm up for a ride? Does the pain happen right away or does it develop over time as you are on a ride? Do you have the same pain if you wore regular non-cycling shorts? I fit one lady who just couldn't get comfortable in tight shorts - she wears running shorts with no issues.

Clipless can make things better, but it can also make it worse. If you've got side-specific issues cleat placement is important to make sure your legs are either tracking the same or tracking to account for any imbalance, be it due to prior injury, muscle or bone length issue.