In my opinion no I don't think there is a difference. It just depends on what specs you want for your MBP. Like for me I had to order mine online because my local store didn't have the 7200 RPM hard drive in stock. If you are just buying the MBP as it is without any kind of upgrades like 4 GB RAM or the 7200 RPM then the local Mac store should have what you want.
Edit: Here's a helpful link https://forums.macrumors.com/threads/326228/
Edit: Here's a helpful link https://forums.macrumors.com/threads/326228/