I think it is because of the general rule of Chazokah - when all things are equal then a person retains his former status. In this case, he remains a non-Metzorah.
The 2 exceptions are exceptions because there's a Pasuk for each one that makes not all things equal.
I think the Yachin on this Mishnah hints/says this:
כל ספק נגעים טהור:
אליבא דכולי עלמא ...
In short, the rational is the rules of Chazaka. My answer is based on the Rash Negayim 4.11.
See Nazir 65b
MISHNA: Any case of uncertainty with regard to leprous sores is initially deemed pure until it is established that it is a case of ritual impurity. Once it has been determined to be a case of impurity, uncertainty concerning it is deemed impure. ...
The answer is Chezkat Chulin (permitted) + Safek if something fell there, lead to permit even for An Isur Deorayta.
The Gemara Yebamot says regarding a berayta similar to our Mishna, that the Kula שאני אומר (because I assume that)
is because of a Rov Chulin (> 50%, not > 100/1). Even if the Teruma falls on the chulin, it's batel berov deorayta. this is ...