Charging for chips would change everything
An oven-baked tortilla is a truly magical thing, and it can be a way to show the customer from the get-go that you're serious about what you're putting in their mouth. The scrappy, penny-pinching 20-something in me is dying a little as I write this, but I would pay for a better chip. In an instant.
In the course of a meal, a couple bucks isn't making a big difference in the bill,. What does make a difference are fresh chips of purposeful thickness served alongside multiple types of salsa, none of which are freezer burn-flavored. Once you've got people paying for chips, perhaps that influx of revenue could offset the high cost of guac and queso, bringing down those prices and encouraging more purchases of tortilla-based aperitifs. Oh, and you can bet your ass that you're not throwing away chips you paid for... and since you did pay for them, you won't feel weird asking for a to-go bag.
Bottom line, I'm happy to reward a restaurant that goes the extra mile and makes its own chips with up to 299 cents, or about one cent per chip I usually consume pre-dinner.