That's a really good point. The thing is, compared to animations down the lines, we're talking about an actual 3d model set that will use all these. I dont believe they'd work on a model and keep it named after joker and only rename the hair animation file.
I mean, if we're talking about a literal copy-paste of all of the character's files to use as a starting point, I think it's reasonable that they'd not bother to change the name of the file containing the animations, but rather just the animation names themselves. Especially since this is clearly a v01 of this file. You rename the containing file once everything in it is finished and it's not a Joker file anymore. Basically, here's what I think we're looking at for Jane's timeline, if she's a different character.
1. Jane is decided upon as a DLC addition.
2. Sakurai and co. decide that the best character to use as a base for Jane is Joker, a recently completed or significantly worked on character.
3. Developers start to create Jane within the existing framework of Joker, using their similar traits to speed up development.
4. The developer working on this particular Jane file doesn't bother to change the Jackc06 file they're working in to simulate ponytail physics because it's still mostly Joker's file, and they're going to rename it to Jane once they're done anyways. However, the new animation is given a Jane name because it's an all-new animation that Joker doesn't have.
5. Game goes gold during this time, accidentally capturing this state of the files due to the glitch and giving us an insight into how this specific development process goes.
6. Code mentioning Jane found by dataminers, leading to this whole debacle.
7. Nintendo notices leak, plugs it with next patch, continues to work on Jane.
Seems very plausible to me.