This method has not been fixed, you just changed the way it works. Using the Momijigaoka -> Mushroom Shrine method takes into account where you last talked to Spinel and entered Mushroom Shrine. For example, if you last visited Mushroom Shrine from Ludibrium through Spinel, it'll send you back to Ludibrium. To fix it just talk to Spinel and visit Mushroom Shrine in Henesys.
Another trick if you have a Mercedes, put the link skill ability onto your preferred character. They can use Mercedes' skill to auto-warp to her town, then use the portal on the right to go to any town in Victoria.
Also, even faster is Xenon, since they can use the Promessa warp to go the aquatic base, then use the same system as the Pantheon portal.