Another thought that may or may not be helpful is that you are basically a minnow being buffeted around by much greater forces beyond your control. Immigration issues are to some extent a political decision. It could be that one of the big chiefs of Keidanren expressed concern to the head of immigration over an agreeable dinner in Aoyama that companies were losing essential foreign workers due to no new ones coming into Japan because of Covid restrictions, and the head of immigration promised to make things a bit easier for existing immigrants, which would work in your favour. Alternatively, the person dealing with your application may be suffering from hayfever and have recently been ditched by his girlfriend in favour of a foreign barbarian, which wouldn't help your case!
The serious point I am trying to make is that there may well be some arbitrariness in the decision and it may be best not to take the decision too personally.
mdchachi - I believe that NI and pension payments are requirements for PR, so immigration must have access to information on payments, either through the local ward office or through My Number.