Shantotto accidentally ended up in Hydaelyn because she screwed up a spell (the same one that kick-started her FFXI add-on pack
A Shantotto Ascension. She stated this specifically during her event's dialogue and even name dropped the add-on pack's title. It had nothing to do with the Mothercrystal. As for Iroha, the exact mechanics for her appearance in Hydaelyn is never explained, she just... materialized here and it was kind of handwaved away as 'magic'. I think the development team doesn't want you to think
too heavily about it and just enjoy it for nostalgia.
If you're hoping that SE will be running crossover events frequently, well, apart from hints that a FFXV event may be occurring, I wouldn't hold your breath - these sorts of events take a lot of resources to develop, which could be better spent elsewhere on the game, and thus would only really be reserved for occasional special occurrences (this event after all is to coincide with FFXI's storyline being wound up - why else did the event start on November the
11th?).