Unfortunately there's nothing that SE can really do at this point short of entirely changing how the Hunt works (at least with respect to current expansion Rank As). The only decent solution I can think of would be for SE to put a timer on how often a player can kill a specific Rank A (similar to how we can only gather one treasure map every 18 hours). That still gives players to go cross world to get credit if they missed the train on their own world (either due to timing or congestion) but takes away the incentive to do more than one train a day.
This congestion is normal for the first couple of a weeks when a major patch is released. This was true even before world visit was added. It will clear up as players get their augment tokens and go back to doing other things.
The congestion problem has been discussed by many of the conductors on Crystal. Many of us are affected just as badly as other members of the train. But we are at the mercy of spawn timers and conductor availability. We do our best but there's always going to be someone left unhappy.
As for trains being conducted by players from other Crystal worlds, that's usually happening either at the request of or with the consent of the main conducting teams from those worlds. Rin (most likely to be the off world conductor you'll run into) has been a huge help in making certain trains are getting run on a regular basis and always keeps other conductors up to date on what's been scouted and ready to run in the conductor cwl.
Problem with calling the Aetheryte first is that you leave the train stuck right at the Aetheryte, causing congestion at that location and preventing players from loading in.
It's better to call a location a short distance from the Aetheryte so players move away and others are able to load in. That worked much better when I was using that system back in SB. There would always be those few players who already knew the mark location and would take off but generally people would manage to load in and make it to the kill (assuming instance capacity wasn't hit).
As for players not being able to get in at all because too many players know about a train, conductors can't control who gets the relays. Everyone has their own set of linkshells and cross world linkshells they relay to, then the members of those linkshells spread the word even more. There's not much that can be done under the current system.