For those who have not completed games in the Xenoblade Chronicles series, this page contains spoilers regarding the plot. Discretion is advised.
The Meyneth Shrine can be accessed after completing the Story Quests Shrine Transport and Pillar Verification Devices. Egil is fought here. After defeating him, when the capital collapses, the party is saved by Miqol thanks to the Junks, revealed to be a ship. They head back to the Hidden Machina Village.
After this point in the story, the Mechonis Field becomes entirely inaccessible. While the maps of Central Factory and Agniratha are inaccessible via Skip Travel, Central Factory is still accessible with the Junks through the Ventilation Conduit and Agniratha is still accessible through the Agniratha Transporter. The inventory of Hidden Village Shop 1 changes and Hidden Village Shop 2 becomes available.