On the subject of supplier rates and statistics

I've been listening to the Doubt and Statistics classes lately, and I've come across a few questions or extensions that I'd like to understand.
I'll ask two of them here, but I'd be happy if there was a general way to ask questions about each lesson individually.
 
In class 32, there was a discussion on the laws of doubt, with an emphasis on doubt from Torah to the severity of Torah or from rabbinic law.
A point that I was missing was the interrelationship of the various methods with the rule of the Gemara, "Every rabbinical ruling is like a law." In my humble opinion, this makes it difficult to explain the Rambam in the way the rabbi explained it. And perhaps it provides an opening to understand the laws of spic spic according to the Rambam's method as well.
In addition, the rabbi brought up that the Rambam studies the law of doubt from the Torah for the purpose of killing a bastard. Thinking further about the sermon, it seems to me that the law can be studied like the Rambam only for places where the boundary of the prohibition is essentially halakhic and not real. Such as the bastardization of milk or blood, and not for prohibitions such as forbidden meat, which are essentially real.
In lesson 33, the rabbi mentions that guilt offerings come for a reality that is not necessarily a sin. I would like to know how this fits with the Mishnah at the end of Kiryatut or in tractate Yoma, which says that Yom Kippur atones only for those guilty of guilt and not for those guilty of sins. How does the concept of atonement fit in a place where there is no sin?
Thank you in advance.
Shlomo Gvirtzman