Difference between Phd degree while remaining a student, and after quitting a Japanese university?
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.