(a) I don't understand the problem? we know from mikvaot and other places that if the mikveh has 40 se'ah - it's kosher evan if rain or somthing else will get into it. So - if the PERAT hes already 40 se'ah - it's kosher anyway!!
(b) another thing: if we say that the PERAT is in eretz israel - that settle the version we learn formerly about NEHAR KEVAR (PERAT) -(karian velo ketivan) and support absulotely the opinon the its in eretz israel. ISN'T IT?
(a) A Mikvah of rain water is only Metaher b'Ashboren -- with still, collected water in one place. Flowing water is Metaher only if it is a Ma'ayan (a spring of natural water and not rain water). Therefore, if there was more rainwater in P'ras then the natural spring water, it could not be Metaher while it was flowing, and it would have to be enclosed in a Mikvah (collected in one place).
(b) This Gemara is saying that P'ras is not in Eretz Yisrael. Rather, those on the shores of the P'ras will be able to see from the waster level if there was rain in Eretz Yisrael.
But, according shmuel in shabat 65b - "nahara mikefie mitbarch" (i.e. from itself). Therefore it has to be that nehar perat has the din of maayan before "sheyirbu hanotfim al hazohalim"!!
Moreover. The tosfot brings us from Ta'anit that against tefah from up there is 2 tefahim that come from down! So, the water from down will make the ma'ayan tahor for mikve (since even if there is 20 and masheu (ketzat) - it's tahor - since rubo is tahor) and there is no different how much rain will get into the river
So, the question above still remains, isn't it?
Your point is exactly the Gemara's question. The Gemara says u'Pligi d'Shmuel a'D'Shmuel, the two Halachos of Shmuel are incompatible; if Nahara m'Kifei Misbarach, then it is Kasher.