Does proper mean completely here?

Here is the number six definition of proper from the Merriam-Webster online dictionary:

strictly limited to a specified thing, place, or idea <the city proper>

In this instance, it means that there is a genetic machinery, and that the basic nature of that genetic machinery is not changed by this expression of genes, but that the expression of the genes causes an effect which is not from the genetic machinery. The genetic code is not changed by the methylation--offspring still inherit the same genome from the parent organism(s). But methylation means that affected genes express themselves, or fail to express themselves, without reference to the basic code--without reference to the genetic code proper. (Please not that this usage of proper always sees the word proper after the word or phrase it modifies--in this case, genetic machinery.)

The adjective "proper", used after a noun, (postpositively) has a special meaning. It means "strictly so called; in its true form", "referred to or named specifically so as to exclude anything not directly connected with", "understood in its most exact meaning". It indicates that you are referring to the central and most important part of a place, event, or object and want to distinguish it from other things which are not regarded as being important or central to it.

Does he live in Chicago proper or in the suburbs? (Chicago proper: within the boundaries of the city)

A distinction must be made between archaeology proper and science-based archaeology. (Archaeology is the whole field and science-based archaeology is a subdivision)

Operating outside the genetic machinery proper - operating outside what is strictly considered to be the genetic machinery.

Excellent.
Thank you both.