Just a quick update for anyone interested, I got a reply back from the Immigration Bureau of Japan. As follows;
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"This is the Immigration Center at "Immigration Bureau of Japan" of "Ministry of Justice".
In regards to your inquiries, we will answer as following.
This is an Information Center being in a position to answer general inquiries such as the necessary documents and the outline for obtaining residence statuses and landing permissions. Unfortunately, but we are not sure whether a bachelor's degree of the online university is acceptable in Japan although there is no limitation on the type of university as for Immigration Bureau of Japan.
When applying for "Application for Certificate of Eligibility" for working in Japan, please consult with inspectors at the nearest Regional Immigration Bureau in Japan through your sponsor company.
Ministerial Ordinance to Provide for Criteria Pursuant to Article 7, paragraph (1), item (ii) of the Immigration Control and Refugee Recognition Act"
日本法令外国語訳データベースシステム - [法令本文表示] - 出入国管理及び難民認定法第七条第一項第二号の基準を定める省令
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Now I have to admit I'm not 100% sure what this means yet, but from the initial email reply I'm taking away that weather an OU/online degree is accepted is purely down to the employer who would be sponsoring the visa / offering the job. Though it doesn't seem there is a list of official/certified unis that are accepted by the Immigration Bureau, it seems it could more just come down to discretion of the person processing the certificate of eligibility on the day. In which case that's a little concerning as potentially using the OU could mean a degree with them might be worthless :/
It might be that I'm completely misunderstanding this, as there seems to be a lot of information in the link they've provided, so maybe I'm missing something, I'll have to read through it all thoroughly and see if I can make more sense of it.