There's lots of delay causes. The trains have to be organized in a certain way for safety and stability, so it's rare to be able to have a perfect first in, last out arrangement. Heavy cars at the back and light cars at the front can cause a strongline derailment on curves. Heavy cars with little coupler dampening at the back and light cars with excessive damping at the front can cause a column buckling derailment on hard braking. Then there's weird slinky physics if dealing with slopes. And then from there, even after all that, it's not just an A to B trip. They stop, add cars, leave cars, send groups on other routes, etc. There's 30 cars going A to B, 40 cars going A to C, cars going B to D, C to A, F to J...
I don't really see much new concern with crossings. Trains already cross roads frequently at high speeds with no effective means of braking in time to avoid a collision. Urban/suburban crossings should already have gates. Rural crossings are hilariously unguarded. I'm not even sure if they all have lights, let alone gates. I'd actually see a benefit to the increased crossing frequency coupled with decreased crossing times. Many collisions are the result of people fearing having to wait at the gate for 5+ minutes as a huge train crosses, so they race across to beat the train. Obviously, people will still try to beat the drone in the same way they accelerate through yellow lights, but maybe they'd be a little less inclined to do so. So, regrettably, the network already gets disrupted frequently. Railroads are very efficient at clearing incidents to reopen the track once all evidence is collected. Trains drive by while wrecked cars and spills are still there.
For one of my local crossings, there's a weekly 10 minute crossing event. The train pulls through a road crossing, stops, reverses down a siding to pick up/drop off 2 cars, then forwards away, all while blocking the crossing of a major road. Seems like a good cooperative way to still service one of those few remaining sidings without making car drivers irate at trains.
I'm not saying this is a valid business plan, but I'm failing to see how this is an "obvious" failure. They of course want to advertise as completely independent drones, but it'd be neat to be able to join a regular consist and get released to only drive itself the last mile.