The Mishna says that chazal made a gezeira to consider all kusim to be nidas from the moment they are born. The gemara explains that the Mishna follows the opinion of Rav Meir who is concerned for the minority against the majority, which requires us to be concerned that they are all part of the mi'ut who menstruate at a very young age. Tosafos assumes that R. Meir's opinion of being concerned for the mi'ut is a d'oraysa concern, therefore questions why this is listed in the among the 18 ge'zeiros in maseches shabbos, which are all d'rabonon. In truth, it isn't so obvious that R. Meir's concern for mi'ut is d'oraysa, Tosafos in Chulin 12a writes that R. Meir's entire concern for the mi'ut to ignore the rov and consider it a safeik is only d'rabonon - דנראה דמדאורייתא לא חייש רבי מאיר למיעוטא אלא מדרבנן. But in truth, even if we assume it is only d'rabonon, it doesn't belong as one of the 18 d'rabonon ge'zeiros since it is a general rule of being concerned for the mi'ut whereas all the 18 gezeiros are specific.
Tosafos explains albeit, not so clearly, that there are 3 levels within R. Meir. In the gemara itself it clearly differentiates between a "mi'ut that is common" to which R. Meir is concerned, and an "uncommon mi'ut" to which even R. Meir pays no attention and follows the majority (in other places this is referred to as a מיעוטא דמיעוטא). However, Tosafos says that even within the "common mi'ut" that R. Meir is concerned about, doesn't apply to a girl at birth because at that age it is certainly a very uncommon mi'ut. However, since at some young age there would be a "common mi'ut" that R. Meir would be concerned for on a Torah level, we make a gezeira to include all girls of kusim to be considered a Nida from birth. Therefore, the concern for mi'ut is indeed d'oraysa according to R. Meir (or according to Tosafos in chulin a general d'rabonon), but to consider her a Nida from birth is only d'rabonon.
Tosafos explains that the gemara feels compelled based on the language of the Mishna to say that it is in accordance with R. Meir, not the Rabbonon. However, the actual din in the Mishna to treat kusi girls as Nidos from birth, even the Rabbonon would agree to based on entire separate line of reasoning. The Rabbonon hold that there was a gezeira made against kusim to prevent them from assimilating and mingling among regular Jews. Even if we consider them to be Jewish, the Rabbonon recognized that there had to be artificially imposed lines drawn to separate them from the regular Jewish community, because there was a fear that they would have an influence on the committed Jews. Non-Jews who were clearly not Jewish weren't a risk to the traditional Jews, but since Kusim were performing some mitzvos, there was a tendency to let your guard down and be more accepting of them. Chazal considered this to be a major threat and therefore imposed on the kusim a stricter status than they imposed on goyim.