The תיובתא on ר' יונתן (Horayos 3b)

The gemara brings a תיובתא on ר' יונתן from the din of רובו ככולו by a גזירה שאין רוב הציבור יכולים לעמוד. The Keren Ora asks why is this a תיובתא on ר' יונתן? After all the only machlokes is if they are silent, everyone agrees that if 1 of the Beis Din disagree with the psak that there is no פר העלם דבר. Therefore, according to everyone you don't go בתר רוב here. The machlokes ר' יונתן and everyone else is on a detail, does everyone have to agree (ר' יונתן) or is שתיקה enough. But everyone agrees that if even one member disagrees you don't go בתר רוב. If so, why is this a תיובתא on ר' יונתן?

The Keren Ora does not have a good answer for the question.