This phrase is a little confusing, let's break it down:
1) One can always assume...
Here, "one" is being used as a pronoun, to describe a person, the subject of the sentence. In this case, the person who is doing the assuming, whether that be the speaker, the listener, or some other person. The meaning of the sentence doesn't change in any case.
The author is saying that one can always assume something. This means that something is true often enough that it is a "safe bet". It might not be true, but it probably is. Consider: "You can always assume that winter will be cooler than summer."
2) ...a little extra buffer...
A buffer, in this context, is a deliberate excess added to account for problems that may arise. This is often described as "padding" an estimate. For example, you expect work to take four hours, but you promise to complete it in six, so that you have a buffer in case something goes wrong.
In this case, "a little extra" means that there is more of a buffer than one would normally expect.
3) ...of paranoia...
In this case, our buffer is due to paranoia, an overwhelming or irrational fear. This is used here as a more intense version of caution. For instance, looking both ways before crossing a street is reasonable caution, but refusing to cross an empty road without a vehicle is paranoia.
4) ..built in...
In this case, the author is describing the action of adding the buffer to what follows. When you pad an estimate, you are building in a buffer.
So, to rephrase the statement:
It is a reasonable guess that in matters of public health, authorities will increase their estimates out of excessive caution. However, sixty days of fermentation still seems reasonable.