Difference between Phd degree while remaining a student, and after quitting a Japanese university? I am currently enrolled at a Japanese university in the doctoral program of Mathematical and Life sciences, and have already been a student for last 4 years. I am waiting for the acceptance of research paper, and based on it, will submit the thesis for defense soon. 

But I came to know that Japanese universities have a system where one can actually quit the university, but if the paper has been accepted, one can apply within one year for a thesis defense. A PhD degree will be awarded in the case of successful defense.

My question is, has anybody here been such a situation, and is aware of a possible difference between the technicalities of the difference in PhD degree, while remaining a university student, and after quitting the university? I know the concerned university or department should be the best place to answer it, but just in case anybody here can clarify that, I would be grateful for it. 

At the minimum, will the degree obtained after quitting the university, would it be considered equivalent to the degree obtained while as a student or not? I guess other country universities don't have such a system in place. Thank you very much.
Disclaimer: my Japanese is quite good, but I'm not a native speaker, so please keep that in mind. 

Based on the degree statutes of your university (広島大学学位規則), you need not be enrolled in the graduate program to submit a thesis and apply for a defense (Article 2 Section 3). However, non-matriculated students must pay a fee of 57,000 JPY for the defense. This fee can be waived if the applicant is not currently enrolled, but has completed the program and left the university without defending within the past year (Article 4 Section 3). If you wait longer than one year you can technically still submit and apply to defend, but you would have to pay the fee. 

I spent 10 years at a Japanese university, although not the same as yours. I can recall one person who got their degree in the non-traditional way, so it is possible but uncommon. 

I assume you don't have Japanese citizenship, so have you considered what will happen to your residency status? I can't recall the procedures, but you could run into trouble unless you have a job lined up and can change your status easily. I would discuss this with your adviser, but I can almost guarantee things will go more smoothly if you just wait for the paper to be accepted.  You may need to revise the paper based on reviewer comments as well. In the meantime, maybe you can apply for positions or spend time making your CV and dissertation look amazing.