Historically, there has always been a lot of misinformation and speculation regarding new vehicle prices. Let me start out by saying that the Invoice price is, despite what many will argue, the price that the dealer actually pays the manufacturer for the vehicle. It is not a fabricated value and it's not negotiable. Dealers are not - despite what many think - buying Raptors for $50k and selling them at $70k for a $20K profit. However, with the variances in prices of new vehicles between dealers that has existed for decades, it's certainly fair and understandable that many consumers are confused and skeptical of the entire process.
As mentioned earlier in this thread, dealers sustain new car sale profitability through hold back. That is the kickback that the manufacturer provides to the dealer for selling the vehicle, and it can be anywhere from a couple hundred to a couple thousand, depending on the vehicle being sold. Manufacturers also offer internal dealer rebates and incentives that the buying public are not privy to. This is of course by design, and allows the dealer to either profit the incentive/rebate or pass it on to the customer for the sale. When you see any vehicle advertised below invoice price without any documented consumer rebates, you are most likely seeing the discount due to a manufacturer incentive. These are most common at the end of a model year when the dealer is looking to clear the lot for the new inventory. The dealer I bought my truck from in London, KY already had it advertised below Invoice. I wasn't about to insult them by trying to negotiate a lower price; clearly they were offering internal incentives to move inventory.
That being said, dealers make the most profit through their fixed operations. Meaning parts and service, where the profit margins are massive compared with new vehicles sales.
Of course, there will always be the dishonest dealers that try and up sell anything they can...undercoating, window etching, anti-theft systems, fabric protection, wheel locks, paint protection packages, etc. They typically rely on the finance manager to sell these add-ons and pad their bottom line as much as possible. If they try and pressure you into any of those up sells, push back and walk away if necessary. If I had a dollar for every single aftermarket alarm I've had to "un-install" I'd be able to buy more than just lunch. They use quick splices (scotch locks) to install these devices, and all they do is damage the factory circuitry. They do not prevent theft; bypassing the module hanging under the dash by connecting the two matching wire colors will still allow it to start (with a programmed key). The dealers buy these "anti-theft" modules from Chinese companies for $5 and sell then for $699 to unsuspecting consumers; it should be criminal.
Another dealer scam is "special editions" or "custom" packages. This includes "Shelby" (aftermarket), Hennessy, SCA Performance, Roush, and Saleen in addition to no-name companies that install cheap modifications for the dealer with the premise that they'll profit tens of thousands on the sale. These are nothing more than cheaply engineered aftermarket modifications with non-Ford approved components that do not perform to OEM standards, are not warranty compliant, and will only cause the owner massive headaches in the future.