Only you can decide what path to take, but it is good to see the potential downsides of what you are doing, because sometimes the feeling of 'I want' can be so powerful that we ignore our own safety and security.
To be honest, yes there is a very good chance that you will experience some level of negative treatment from people who know or suspect that you are transgender. You could be surprised and the people whom you thought would react negatively could be very supportive, and vice versa. Also, there are some people who will probably act nice to your face yet talk behind your back, and beware of anyone who is too curious - sometimes they may have a desire to spread gossip, thinking it's just 'interesting' but not realize the harm that their talking may do.
People may be afraid to get sued or fired if there are discrimination laws in Japan so maybe they will avoid saying anything negative to you, but they could begin to feel uncomfortable in your presence (let's be honest, many cispeople have issues with homosexuals and many many more with transsexuals). They may even talk behind your back, and there is a chance that you could find yourself losing opportunities for advancement, even if you are never directly fired -it's hard to prove them wrong or fight if they claim someone else was better suited for the position.
If you're worried about the fact that you might get poor quality care then you can always switch doctors, but seeing that your trans on your medical record can result in losing the respect of many doctors - I've had bad experiences EVEN AT EMERGENCY ROOMS. Yet if they don't outright deny you care or use slurs then you won't be able to sue - they can talk to you slowly like you're mentally disabled and reassure you that 'nothing is wrong' when you have serious problems, etcetera.
The reality is that being trans is WAY more complicated than people make it out to be, and it takes years to see the full effect because much happens out of your sight and hearing, and there are only certain situations where this will be presented right in front of your face.
Just think hard and remember - you can always do it later, but it's much harder to go back