This would at least help to understand the Rambam who does hold that ביעור is only at the time of the prohibition and yet he gets lashes [because obviously he is going like the sages against R Yehuda] But the thing you see in the Rambam is the way he understood the argument between the sages and R. Yehuda--is what is the destruction of leaven? Anyway possible or only by fire? But both hold it is at the time of the prohibition. So this is how Rav Shach understands the Rambam and I think he must be basing it on that later Gemara.
Of course, none of this is like Rashi or Tosphot. And that leaves us with the obvious question what do Rashi and Tosphot do with that Gemara on page 93-95?
In any case there is clearly a lot of work that needs to be done here. Reb Chaim Soloveitchik also deals with this same question but I do not have his book nor the Gemara. At any rate his answer, is that לא יראה ולא ימצא is a positive and negative command--so that is how he answers for the Rambam which does not help us about the Gemara on 95.
In case it is unclear what I am saying here it is this. You can not have לאו הניתק לעשה when the עשה starts before the לאו. They have to start and end at the same time for this law to apply.