I'm sure there is a difference after having an ISF calibration done. The question is, can you realize enough of a difference to justify the cost?
At $200, I would consider calibrating my 720p projector. I don't think I'd pay $200 to calibrate your 40" LCD. I have the 46" version of this television (550 series), and I love it. I have looked at some calibration settings from using avia, DVE, and get grey, as well as used the settings that others have posted for this tv on avsforum.com. I don't doubt that a professional calibration would improve the picture, but I can't believe that it would be worth it to me. At 40", instead of 46", I would say that this is even more true for you.
If you want the very best possible picture of any 40" tv, you're probably not looking at the right model. If you want the best VALUE, this tv is probably right up there (though I'd prefer the 46"), and it probably doesn't make sense to add an ISF calibration if you're looking for bang for the buck.
And even if you are, I am having a hard time believing that Best Buy would be a good provider for ISF calibration, regardless of the tools they use.