It would surprise me too in Japan went for Typhoon, but...
The requirement is for air defense, which is why they wanted the F-22's acceleration, speed, altitude and load-out. Typhoon is closer to the F-22 in those respects than anything else.
The Super Hornet is good for a lot of missions that JASDF is not going to do with this aircraft (like CAS and FAC-A) and is certainly not the world's speed champion (although the EPE engine and conformals help). The USN, on paper, also plans to start retiring it in 2030. They won't, of course, but questioning the program of record means questioning plans for the F-35C, which is non-career-enhancing.
The F-35 still has no fixed acquisition or operating costs, or IOC date, and equally is not going to win speed records. In stealth mode it carries four AIM-120s, and radar aperture is smaller than the Typhoon.
Result: turning down the Europeans has a higher-than-usual price tag for Japan.