As mentioned in the article, Japanese society favours stability and predictability, life-time employment is something that has been the standard for a long time and your elders and society at large simply won't accept you if you don't have permanent full-time employment. This means a harder time to get everything from an apartment to a credit card. You have deviated from the true path, which is to secure employment in the "job hunting" period, which lasts for about two years leading up to your graduation as a bachelor or a master student (Ph.D. is generally a different story, so let's save that for a different time).
This job hunting involves an initial one year of "getting to know" (the companies do take attendance) each company at seminars and events. You register at their websites and attend in your own spare time. Schools try their best to respect this and are not as hard on the students during these years. Hordes of students dressed in suits (mind you, there is one kind of correct suit for this, well, one, depending on your gender) try their best to learn about the company and their goals, because this step is the preparation for the second stage. The second stage is filing applications, we are now somewhere between 1 1/2 and 1 year prior to graduation. A student can apply for as many as 75 companies, the reason for this will soon become clear, the failure rate is high and so are the stakes. At this stage the student has some idea of what he or she wants to do, but they will apply for anything they can consider okay. Each company has a different time when they accept applications and then go through three, four, maybe even nine steps of tests, interviews, group interviews and procedures (public sector jobs usually has an exam with questions from history and English to IQ-testing, you need to pass to get to the next stage). Once a student gets past these steps, they get an offer and are faced with the choice of accepting it or maybe to wait since their dream job may not even have started accepting applications yet. Once you enter the company you may very well receive training that is very different from your educational background, you are now "one of the family", for life, but that is a different story, let's get back to the start-ups.
Now, how does all this play into the start-up scene? Well, the one correct way to go through job hunting is when you are about to graduate. Some students fail to get a job, if you are a bachelor (this I am told holds especially true in science and engineering), you beg to your parents to fund you through your master and you then try again once you are done with your master (if they are rich enough, it isn't cheap and same thing goes for Ph.D.;s). Being outside the system for a year without a very good reason, such as interning abroad, will label you as an outcast, making it difficult to reenter the system. The same, of course, holds for those that try and fail to take part in a start-up. This creates an enormous disincentive to take risks and I think plays a major role in why the only successful Japanese start-up that I can think of that has gone big in the last 20 years or so is Rakuten. I can't blame students for simply asking, "Why should I take the risk? Why should I build the companies of the future?".
This is turning into a speech (maybe I am entitled?), but the way foreigners fit into this whole mess is that we, to a large extent, are exempted from this honour system. We are not expected to "understand" the correct way and can more easily jump between companies and most of the smaller start-up;ish companies I know in Tokyo are at least 50% foreigners (I think I may be a bit biased here). What I suspect is the attraction for foreigners is the culture and the challenge, maybe also the good (and diligent) labour. I think it was Bertrand Russel that said that Japan doesn't move ahead at a continuous pace but rather by skipping ahead after a major collapse of the foundations of its society. The Meiji Restoration and the end of WWII springs to mind. Only then has it been demonstrated that the old ways have failed and there is a climate where innovation can take place on a grand scale and companies and society can be resown. On a personal note, I hope that it won't have to be quite so dramatic, but the whole situation surely is problematic although getting better and better over the short amount of time I have been here.
If you got all the way to the end, thanks for staying with me. Having been in Japan for a few years now I tend to reflect upon these things. The above opinions are of course biased by my own limited understanding of things, I am an amateur at best, but maybe they can prove useful.