The real regulatory risk of the JFSA is that they ask the 6 cryptocurrency exchanges to enhance their operation by 23 July 2018 - In the event that they fail to do some by the deadline further action might be taken against them.
Well capitalized players like Bitflyer should have no problem in enhancing their operation - They can easily do so by hiring some consultants and lawyers.
Smaller cryptocurrency exchanges may worry the market as they may not have the resources to comply with all the requirements while maintaining their bottom line.