It's unclear exactly when Troi was promoted to Lieutenant Commander.
Riker remembered her as a "Lieutenant" in "Encounter at Farpoint" - that is, he initially called her that, despite her new rank pins. This would suggest she had held Lieutenant rank when the two last met - meaning 2361 or later if "Second Chances" is to be believed. So we could argue her rank of Lieutenant Commander was basically brand new in 2363 when "Encounter at Farpoint" happened.
As for the departmental color charts of ST:TMP and ST2 through 6, artist intent is one thing; onscreen reality is another. The TMP chart may hold for the most part, because it was just one movie, but Fletcher's colors for the next five movies plus the odd TNG or VOY flashback were mangled by so many costuming department decisions and mishaps that they probably aren't to be trusted as such.