The phrase "are we clear on that" is one that would typically be used in the context of a power difference. To use a military setting, a general might say to a major, "Listen, we are not going to invade Crete. The discussion is over and I don't want to hear another word about it. Are we clear on that?" Here the general is expressing some irritation and he's "pulling rank" on his inferior. A major would never use the same expression to his superior the general, unless he wanted to risk being written up for insubordination.
On the other hand, to use the expression "it's clear to me" doesn't necessarily carry the same connotation. It would be perfectly polite for the major to say to the general, "Sir, based on my review of the intelligence, it is clear to me that to invade Sparta would be ill-advised." Here the major is using the phrase to mean that, after review of other material, he has arrived at a conclusion that he feels is sound.
