I am not a grammatician, but I will try to explain as I understand it.
I don't think that knowledge is countable, because you cannot have one or two or three knowledges, that is not a proper usage of the word.
However you can have a greater or a lesser knowledge.
I don't think that the indefinite article 'a' stands for 'one' in this case.
Rather I think the 'a' is used here to express that you have some amount of knowledge versus none, or to specify what kind of knowledge (this kind versus that kind).
What kind of knowledge will they have? A working knowledge. You could not say as an answer to the question just 'working knowledge'.
So she is saying that by the end of the training the person will have some amount of knowledge, or a general knowledge (that is, not an in-depth knowledge) of the material or of the subject.
The 'a' is used in a case like this above where an adjective is placed before the word knowledge, to specify what kind of knowledge they will have. It will be a working knowledge (that is, a basic knowledge, a small knowledge) versus a thorough knowledge (that is, a deep or great knowledge).
You can also say
I have some knowledge of Biology, but none of Nuclear Chemistry.
I hope this helps.
: )