When I read these threads, I often wonder just what some people think the margin is on bikes and bike stuff. I assure you it's a lot less than is often implied here. This is America so I've no doubt there is a millionaire bike shop owner somewhere, but I've never met one ... and I've worked in bike shops in the US and UK.
So, if you shop by which store offers the best discount but just a shrug when you go back with an issue, then the discount's worth nothing.
The brands you mention have completely different marketing strategies so you cannot compare. They also have warranty support policies which are incomparable between the two brands, at least in practice. Only one of these would be considered a premium brand and margins on that quality of bicycle are less than one which is built down to a price.
Ignore discount as a criterium. Most stores will offer it to some degree or another. Once the sale is finalised there won't be a big difference in the amount discounted between shops, but there may be a huge difference in the post-sale support you receive between one store and another which may or may not be worth the usd20 you might save. It's up to you.
Shop where you feel most comfortable and where staff take an interest in you and look pleased to see you back. You won't regret it.