Having the scene on the train where Maggie Evans changes her name to Victoria Winters flow into her disembarking the train, hitching a ride with the hippies, and then arriving at Collinwood as Vicki and not Maggie does come off as odd as edited. Clearly Collinwood is expecting a Vicki and not a Maggie. But what if Maggie didn't fill out the application before she traveled to Collinsport? What if Josette's ghost, who obviously has influence over her, persuaded Maggie to go to Collinsport first and then contact Elizabeth? Then Vicki, as it were, may have even called Elizabeth from the train station, and she may have even been in Collinsport for two or more days, giving her time to fill out the application and get it back to Elizabeth before she went for the in-person interview. The film as edited certainly doesn't make it seem that way. But judicious editing can make a lot of things seem different from the way they were originally intended in a script. And in at least one case that we can definitely point to in the film, the flow of the editing, particularly Vicki unpacking her suitcase before Josette's ghost tells her that "he's coming," makes it seem that Barnabas arrives on the say day that Vicki does when, if one is paying attention, that cannot be the case because of everyone at Collinwood wearing different clothes. But if one doesn't pick up on the clothes, one definitely gets the strong impression it's the same day. Who knows if there were actually scripted scenes that would have made the name change more logical? We may never know.
And while we're on the subject of possibly missing scenes, there are at least two other interesting questions about Vicki's initial arrival in Collisport/at Collinwood. 1) Where did she get the money for the train ticket? And probably more importantly 2) How did she obtain a suitcase of clothes that she arrives with? We clearly saw Maggie escape from Windcliff with just the clothes on her back - the soaking wet clothes on her back, in fact. Yet a well put together Vicki travels to Collinsport and arrives at Collinwood. So, could it actually be that scenes are missing between Maggie seeing the notice in newspaper and the train ride to Collinsport? Might have Maggie gotten a job at the diner we saw her in after her escape? If so, that could explain where Maggie got money for the train ticket and the clothes - and it would also explain why, when Bella Heathcote was cast, her character was frequently referred to as a waitress who Barnabas falls for. Again, though, we may never know.
A sometimes unfortunate fact of filmmaking that happens time and time again is how scenes are often removed from films because the studio, the producer(s), and sometimes even the director feels that even though they imparted important info, they were cut because it was decided that they slowed down the momentum of the film. I've heard that said many times during DVD commentaries and/or featurettes. So, perhaps that's what happened with many of the known or presumed missing scenes in the Depp/DS film.