Many companies only want PR holders and a working visa is not enough anymore
I've seen this trend getting stronger over the last few months of my job hunt... When you apply to a company using their online form there is often the knockout question "Will you now or in the future require support with your visa?" which already shows the tendency that they prefer people who don't need support. (I find it really weird too that they flock people who don't have a working visa yet and others who do already have a running working visa but will need a little support for the renewal together, as the second case is much easier and less risky for the company)
Recently the knockout questions get even more direct and just ask "Do you have permanent residency in Japan?" which signals that if they have a enough applicants who are permanent residents they will probably not even bother looking at anyone who choose "no" here.
I know some people don't believe that knockout questions are radically deciding the fate of an application but I worked in the past for a company who actually designs these online application web forms and asked my boss about it. He proudly said that they have many clients who totally use these questions to filter out applications, in some cases the reply to the knockout question auto-rejects an application before a human even sees it. For example with new grads the web forms that make you choose your university from a drop down list, you can expect that certain universities (like F rank) are instantly auto-rejected no matter how good you did in the SPI tests etc.
So recently having several companies having a knockout question for PR might be a new gatekeeping trend that makes it impossible for some professionals to get certain jobs. Some companies are so afraid of the "visa sponsorship" (even though it is really not that difficult at all), that they would probably prefer an applicant with PR (or Japanese passport) and only 3 years of relevant experience over someone with "only" a working visa but 6 years of experience. With the rules on PR getting stronger this will create a huge gap between the lucky ones who got PR before the rules changed and the unlucky ones who will not even be considered even though they already worked for years in Japan with a working visa.