There are many reasons that two cars can appear identical upfront, but have two different prices online, and the problem for the average used car shopper (You) is that these factors simply are not included in online listings.
So, unless you get a dealer that tells you everything without coming in to the store (Good Luck), or unless you plan on personally inspecting every car you are comparing (Not likely), you should remember that you are not comparing apples and oranges when you begin your negotiations.
If you acknowledge that upfront,you will appear far more educated as a consumer and could potentially remove that as something that can be used against you to keep the price elevated.