I've seen my values for known characters and known words and phrases on my progress tab are quite different.

Which one should I use as a yardstick to know which level of Mandarin Breeze or Mandarin Companion readers is for me?

I know I can try to read the sample texts, but I would like to use skritter's metrics to estimate how far I am from a given level, not just whether or not I'm ready for it.

In general you should focus on the word count as it represents how good your Chinese is much better than the number of _different_ characters you can read. That's especially true for advanced learners, because many words use combinations of common characters with quite specific and non-obvious meaning.

That being said, many texts for learners only tell how many characters you should know to read them, as a proxy for your vocabulary.