First, I think he's thinking those cars can be wider than they really can be. If you really put a Jersey barrier between the train-lane and the car lane(s), and don't put the Jersey barrier entirely within the car lane (which I guess you could), he's allowing less than 12 inches of clearance between the edges of the lane and the car bodies. Tractor trailers are the same width as railroad cars (more or less) and they feel like they pretty thoroughly occupy a lane. Having something 2 feet wider than that zooming by next to you at 100 mph seems...not entirely safe.
In any event, the history of attempts to use other than standard gauge is not the sort of thing to inspire one to attempt doing anything other than standard gauge, as appalling as that is. OTOH, if you _really were_ to convert the entire interstate highway system to this thing, you'd probably have put down so damn many miles of the new gauge that it might actually have a real chance of dislodging standard. I don't know.
Second, I think for a laundry list of reasons (several of which he enumerates) this isn't a great cargo/freight system. If you treat it as a passenger + light/high value cargo (like FedEx/UPS/USPS, anything you might contemplating sending as air freight), most of those problems go away.
Third, I think he has skipped right over a couple of severe problems. One is what do you do if you want to, say, go from Las Vegas to Seattle. You're really going to make everyone doing that get off of one train and onto a second? Really? Because you think you can avoid swapping cars around this way? All right. Does that then mean when you're running a through train Boston to Seattle on I-90 you're really going to run that many empties through the big empty of South Dakota and Montana?
Really, I think what would happen is you'd do your absolute damndest to make sure that all your facilities for re-arranging the cars that make up your trains happen OUTSIDE of major cities. Not necessarily a long way outside of major cities, just far enough out in the burbs to avoid trouble. The downside is that everywhere there is a junction of two interstates (which is where you really want to make it possible for through passengers to switch from one interstate to another without getting out of their nice, warm sleeping compartment, navigating a cold platform station and getting onto another train and settled into another sleeping compartment. While still sleeping it off from a long weekend in Vegas.), there is also a mall and similar development. I still think it can be made to work, especially if you initially focus on getting the freight cars and the sleeping cars through the junctions without forcing stuff on and off cars. At night.
Fourth, 100 MPH sounds really fast, but if you're really stopping at all those overpass stations, you're never going to get up to that speed. Like the Northeast Corridor, you'll probably be running some stop-little (express) and some stop-a-lot (local). How do you manage that?
I think here, you just plan on taking over more lanes: the innermost lane is the through/stops-a-little one, and the outermost is the local/stops-everywhere one and there may or may not be more in between those two and possibly the ability to switch from one lane to another. Major signaling stuff required, but probably worth it and no worse than tractor trailers passing each other. Probably.
Fifth, and probably most important, if you really are going to run any cargo/small-box containers on this system, how do you get them on and off? Any vision of a simple platform at the overpass with a minimalist elevator for ADA + stairs for everyone else gets shot all to hell and gone when you start needing hoists to get containers on and off. (I'm ignoring the how do you deal with bursty traffic, because I'll allow an assumption of a really sophisticated web-oriented dispatch system so stuff only shows up when there is space for it ready to go. It won't really work, but hey. I'll humor him.)
I think all of these are solvable. But I think they all involve the nasty unpleasantness of actually having stations, switching yards and dealing with making up trains. The good news is, there are going to be a lot of big parking lots available for this purpose in the world he's imagining.