That's the rigth thing to do, the order in which you do things doesn't break the route after the progress dev stops talking afaik. If you can already use the portable menu, the way i like to think about it is similar to the first part where you need to skip the trigger, before i figured out what to do, I had originally tried pausing but that did not work probably cause rpgmaker prevents it. The jump in the old game was added externally which is probably the reason it can cancel triggers.
Once you figure how to use the portable menu the question becomes which triggers may be helpful to cancel.
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I forgot to say you should save in the cathedral. You can't escape the devroom unless you do something before hand. I think if you interact with the tree at this point it gives you a hint about needing to go outside the normal bounds of the dev room in more cryptic words. Play around with the teleportation orb in the new cathedral, you'll realise there's a place you haven't been before in this route. This room has something special that no other room has.
Wait, I thought that the teleporter in the "modern" section always teleports you to the house of the guy that gifts you the gold dust in the "modern" section?
Oh no... did I do something wrong by getting the gold dust beforehand?
Edit: No, I didn't. It doesn't matter.
Update: WAIT! Is it the doorway that leads to the bedroom? (It is!)
Update 2: I completed the route!