Nothing wrong with either Trek or Giant, would go for the one with the best fit, they are right that it doesn't matter too much about brands much as there are very few bad bikes out there.

Buying from a LBS has the advantage that they can get the bike fitted to you, and if there are any aftersales issues it's easy to get sorted.

For the 'soft tissue' issues, if the inital fit is good, this shouldn't be an issue, would budget for a couple of good pairs of shorts if you don't already have them.