I think one thing that would DRASTICALLY improve AI driving is for the AI to pay attention to not just the direction I'm driving, but also the SPEED. For example, I've got a long bridge over a lake, followed by a 90 degree turn once back over land. When I drive it, I go full throttle over like 90% of the bridge, then hit the brakes, take the turn carefully, then start accelerating again. When the AI drives the same route, it tries to FLY around that turn, at best hitting the rail and having to sort itself out, at worst flipping itself completely off the highway and requiring manual correction. You can get around this to some degree by adding "pause" waypoints in your AI path, but if a route requires a lot of turns, that can drastically increase the time it takes for a truck to go the full loop.
If the AI actually paid attention to the SPEED I was going when recording the loop, it would do a much better job of driving like me, rather than driving like Evel Knievel with a death wish.
As for your specific issue, I've found a decent workaround is to set up my truck stations back-to-front instead of side-to-side, with the truck stations in the middle of the enter/(un)load/exit loop. That way the stations themselves act as dividers between their own loading zones.
You've still got to worry about trucks trying to take turns WAY too fast, but you can get around that by not putting more than 4-5 truck stations on the same straight line.
Here's an MSPaint diagram of how I've got my truck unloading depot setup. Orange outlines are stations, solid orange is loading zones, blue are truck routes, black is my foundation.