The מנחת כהן is addressing the RT in שיטה מקובצת, or just the general שיטת ר״ת in Tosfos? His words in שיטה מקובצת is definitely showing the other interpretation.
I’d have to check if he brings it down specifically, but he very emphatically says it regards to the view of חכמי ישראל, so I see no difference.
I do not think RT would’ve said that if he knew what we know today.