@Patrick Goswitz what's the end goal? Saving money I assume, if that's the case what does it matter if you're getting bids and going with the lowest bid or are you going with a contractor you know and trust? Either way for me they should be able to make their money however it is that they make their money, especially if you find a contractor you like, trust, and want to come back?
If you get 3 bids and for easy numbers sake lets' say you get $3k, $4k, and $5k as the bids, but choose to go with the lowest bid and then tell him you want to buy the materials to save the money yet that's where he's cutting his costs to obtain your business you're still kind of cutting off your own hand despite your face right? I don't know, I usually get 3 bids and go with whom I'm comfortable with, it's less heavy lifting in the end that you have to do anyway. Plus if something is forgotten are you going to run to the store everytime they need a box of screws or something?
I do most of my own work, but when I contract stuff out I let the contractor purchase their materials, besides they know what they want and need. Would you purchase your HVAC stuff and then have an HVAC company come in to install? Just some thoughts