You are correct in your understanding that the perfect progressive (or perfect continuous) is used whenever there is incompleteness in the action, but you're missing two important points:
The first is that the perfect progressive can also have the meaning of "recently" or "lately." For example, in the sentence, "I have been feeling ill." I might actually be feeling fine at the moment.
The second is simply that in conversational English sentences which bend (or sometimes flat out break) the rules are still used, and can become so natural sounding that they're considered perfectly acceptable.
Here's a look at the examples you listed which appeared to contradict the meaning of the verb tense used:
I have lived here for two years.
I would say "I have been living here for two years." The acceptability of your sentence is simply due to its wide usage. Present progressive is the technical choice here.
We have eaten breakfast together every morning since our honeymoon.
This one might actually be correct both in technical and colloquial speech, but perfect progressive would be as well. The action you're describing here is [eating breakfast together], which is something you're not currently doing. You've given specific times at which these events occurred [every morning since your honeymoon], so you're really talking about a series of completed actions. This one's tricky -- I can definitely tell you both would pass for acceptable wording.
However, were somebody to say to me, "Would you like to join me for breakfast tomorrow?" I would probably answer, "Sorry, I'll be eating with my husband as usual. We have been eating breakfast together every morning since our honeymoon." since the continuation of this pattern is actually the focus of my sentence.
Again, I don't think either wording is going to raise any eyebrows regardless of context, even in educated company.
I'm exhausted. I have been painting the ceiling.
This is that other use of perfect progressive I mentioned, that these are the actions I've taken recently. The regular perfect tense implies that the painting is definitely concluded -- "I have painted the ceiling, so we only have to do the walls tomorrow."
You can also add a duration on the end with perfect progressive which you cannot do with simple perfect. "I have been painting the ceiling all morning." This sentence would probably be said around noon; the actions should have started at some non-specific point in the past and continued until now. If it's already evening I would instead use the past tense, "I'm exhausted. I was painting the ceiling all morning."
I had been working on my novel when she entered the room to talk to me.
This one is actually past perfect continuous while your other examples were all present, so its rules are a little different. The past perfect continuous means that something started at a point in the past, and continued all the way up to another point which is also in the past. With the past perfect continuous the action stops before the present -- it always has an end point. In this example, the end point was when she came in to talk to me.
The regular past perfect must reference an action that was already complete when she came into the room ("I had written three chapters before she came into the room to talk to me.") It is also different from the past continuous tense in that the focus is on the activity of writing rather than on what was happening the moment she entered the room "I was writing when she entered the room to talk to me" is perfectly correct and describes the same situation that your example did, it just isn't putting the emphasis on the same thing.