Who's to say Ford can't "markup" either? To me that's exactly what it is...non-negotiated. If the dealer can sell a Mach-E for $5k above MSRP, Ford is leaving money on the table. Ford can bump up their non-negotiated price just as much. Why not? What are you going to do, go to another dealership and negotiate?
I can think of a handful of questions that need to be answered besides just saying "middle man bad".
What's the cost of delivering dozens of vehicles from the plant to a dealership vs delivering one off vehicles to a house? Or the cost of an OEM having their own employees distributed to answer questions on a vehicle. GM has more than 4000 dealerships...would sales decrease because it would be less accessible to customers to see, test drive and service vehicles?
I don't believe the current dealership model of huge lots, tens of employees is efficient. But I'm not so certain an OEM handling everything themselves is optimal.
Just getting on a centralized waiting list would have been 10x easier and more user friendly.