Here are the two concepts that cannot be separated: 1) "...it is possible we understood the phrase “honest loyalty” differently..." and 2) "I had understood the President to be requesting that we drop any investigation of Flynn in connection with false statements about his conversations with the Russian ambassador in December. I did not understand the President to be talking about the broader investigation into Russia or possible links to his campaign." (Source: "Jim Comey Backs Up Trump’s Story, But It’s Not All Good News for Trump.")When taken together, it indicates that Comey understood that he, Comey, did not know what President Trump was thinking in the first case but assumed he did in the second. All we have from Comey is that Comey took something Trump said to mean something when it didn't necessarily mean it. Trump's language regarding Flynn, his words directed at Comey concerning his, Trump's, desire regarding Flynn, did not have to be taken by Comey the way Comey says he took them.
At this point, I have to say that had I been in Comey's shoes, I would have probed the President on exactly what the President meant. I would have explained why too. There is no way I would have allowed the conversation to end without knowing whether or not the President was aware of how his questions and/or statements could possibly be taken and that I had no choice but to pin him down to be sure one way or the other (for the sake of the nation and certainly not in any way prejudging what the President was intending). If I had received the wrong answer, I would have resigned on the spot and gone public.
I can also say that for the foregoing reasons, there is no way in Hell that I'd even begin impeachment proceedings based upon Comey's statement. I'd take that position no matter who the President is, no matter what his or her ideological beliefs, no matter how much I may or may not agree or disagree with him or her.