I'm a fairly new startup and I've been thinking about the same thing. I am considering telling them if they buy their own materials from someone other than my supplier, that I will charge 25% of the cost of materials in additional labor, simply because I don't know what I'm getting into (poor selection, poor materials, etc.), and I may add 10% even if they get it from my supplier because, lets face it, if you buy $2000/month worth of materials, you (we...the contractors) will get better selection and more care loading, etc. than a homeowner that spends $300 one time a year.
I suppose if they get a good enough deal to offset the 25%, then I'm OK with charging more labor for the CHANCE of a little unnecessary work. :cheesygri