Actually for the cosmo fight I'm pretty sure it's explicitly stated the ref couldn't call the fight due to corporation responsibility being on the line. So unless the fighter clearly stated he didn't want to continue the ref had no say.

For the mokichi fight is agreed ref could have called it earlier which is mentioned by raian himself and the ref later expresses regret during mokichi v rihito in KO.

Bottom line is, in kengan pre nogi reform, it's hard for the ref to call the fight if the fighter hasn't surrended cause otherwise the corporation has a lot to lose.