It's a surprise result but, the ignorance aside, the Japanese system is very different to western countries. This result is unlikely to happen against a select university team from maybe any other country.
Players don't just go through youth teams into the first teams at J1 and J2 clubs, most players don't fall through the cracks like in other countries either due to being undeveloped by mid or high school age and cast off by pro youth teams. There are FA academies in place, high level private schools, organisations, and many will ultimately go to university from school and then, when they are early 20s, they will move to a professional club if they are good enough. Some rare 'late' developers even go from high school to J1 without ever setting foot in a pro club academy. But most go the private academy and/or university route.
University football is a key part of their pathway as pros and development as players and the technical level is pretty high, maybe J2 level for some teams.
I guarantee you will see players from this team as pros, maybe even the majority of them, and maybe some in European football one day. If you look at any random Japan U19 or U20 squad it will invariably have several players from university teams.
Some 'long route' ex-university players include Keisuke Honda and Shunsuke Nakamura, and more recently, Kaoru Mitoma, Junya Ito, Ref Hatate, and Hidemasu Morita.