Are there any differences in the quality of products sold at contractor's supply store vs. big box hardware stores?
The first thing you need to understand about "allowances" on any building job is that those are usually way too low to equip the real wants of the buyer. When talking lighting, most lighting supply houses have a "spec" line of fixtures that contractors use to figure the allowance. They are typically the least expensive fixture for the application. When you go in to select lights, you are usually seeing consumer list prices, not the actual price us contractors pay. You could easily pick out nicer designer models and spend 3 or 4 times the amount in your allowance. This is common.  The smart consumer would take the discount and shop your fixtures for what you want at the price you want to pay.  The box stores obviously don't carry the real upscale designer lines, but most of the products are very serviceable, good quality, contemporary popular styles and should last you years. If you are a good internet shopper, you can find high end lighting, solid brass, brushed nichol, stainless, crystal glass, etc at very reasonable prices. Always remember, beauty is in the eyes of the beholder!!!