nor for that matter
Solution 1:
I think OP's example is not very well-formed.
In a nutshell, the problem is but then nor and but nor for that matter both mean effectively the same thing. It doesn't really work for me when nor is being used by both constructions at once.
Having said that, the intended meaning is clear enough. Simplifying,...
1: He didn't go, but then nor did I
2: He didn't go, but nor for that matter did I
3: ?He didn't go, but then nor for that matter did I
...all mean there's nothing particularly surprising about the fact that he didn't go (I didn't go either, so it's not like he did something really unusual that no-one else would do).
Solution 2:
Seems like the question is about meaning more than punctuation. If so...the sentence says
- He had not uttered a sound while the punishment was administered.
- I had not uttered a sound while the punishment was administered.