She won't be able to work in the Japanese system but perhaps outside of it.
I'm also in Allied health and I created a practice here. OT stands a lot better of a chance than PT for that to work (I'm an SLP), and in fact the last time I spoke to an OT here she was begging for info about other OTs in Tokyo to whom she could refer patients.
PT might be just a bit too medical for it to work. Your girlfriend should try to contact the PT association and ask about specific requirements for working with expats who do not speak Japanese and do not use NHI. I feel like I remember a friend (Japanese medical professional) telling me that they had a foreign PT who would come to their clinic and use a room a couple of times per week to work with expats but it might have been a psych or something, I don't recall with certainty. I used to know the president of the PT association chapter in
Okinawa but it's been a couple years since I've been there.
As an SLP it's a bit of a gray area but the Japanese association of speech therapists recognizes that we exist (non-Japanese certified professionals from other countries working in Japan) and just points out that to accept NHI one requires Japanese certification. When my business plan was vetted by the licensing and permitting department of the company which handled my company formation they determined that since what I do is primarily educational and specialized instruction it was legitimately within the law and I did not require any additional Japanese certification of permits (of course I have state licensure and national certification in the USA).
If she wants to do this she needs to do a couple of things. First, she needs to get to the specifics of what is and is not allowed. Second, she needs to determine whether there is a large enough customer base where she intends to practice. Third, she needs to decide if she is going to try to sponsor her own visa.
I would absolutely not recommend trying to start a practice in Japan which would sponsor her visa unless she is prepared to commit a significant amount of financial resources and many years of her life to making it work.
I can't honestly say for sure that I'd do it again if I knew what I know now, even though the business is profitable and I enjoy living in Japan. It's a metric ton of work and the exacting and specific requirements of company record keeping, taxes, etc. are difficult to comply with especially when it is all in a second language. The only reason I can manage is because I'm lucky enough to have surrounded myself with Japanese professionals of quite high caliber, though it's fragile since if I lose one I'm in a world of hurt.
That said, there's more than enough need for my services and within two months of getting my visa my business was profitable. I'm currently looking at hiring since I'm turning away clients for lack of time (other things are also very important to me, so I'm protective of my time). I imagine it's similar for PT.