The weight of suffocation by inaction is weighing down on Isabel/Owen enough that she finally externalizes it again for the first time since being told by Tera/Maddy about the Midnight Realm, screaming for help and yelling that she's dying but nobody can hear her/relate. While it's an incredibly isolating event it leads to her realizing that nobody else is going to help her so she has to help herself, she has to do something, she can't just stagnate like she's done for 40 years. I saw the scene in the bathroom as her finally confronting what Tera/Maddy said and seeing that, yeah, she was right. Owen's body isn't her body. What she felt before about her insides being ripped out and replaced was right.

I feel that the very last scene was written to be as open to interpretation as possible with the knowledge of what had just unfolded but I saw it as the start of Isabel's new beginning/escape.

Personally I didn't get the same emotional reaction to the movie that a lot of other people seemed to get, but that may be because of how I see myself and where I am in my own transition. However, I think that if this movie had come out before I started to transition I'd have a stronger reaction.