Nowadays historians are a lot better about avoiding the tropes of American exceptionalism in their narratives, though I won't suggest that it's a completely solved issue. Some authors specifically try to contradict ideas of American exceptionalism in their research. Whatever the case, a good research work will discuss such matters in their introduction or conclusion (or both).

But I have a couple other points to make, the first of which is that there is no way that the US "really was." The idea of a single, objective truth in history, where the historian's task is simply to uncover the one "true" history, hasn't been accepted in the profession for some time. Historical research is based largely on interpretation. This is not to say that nothing can be known or that historians are just writing bullshit, but rather it suggests that history can have numerous concurrent interpretations which are all valid and based on hard evidence.

Next, I want to suggest to you that the idea of American exceptionalism has not just affected the way historians have written about it (and many older narratives are rife with it), but it has also affected the way American history itself has played out. Americans have, generally, believed in their own exceptionalism since before there was a US to speak of. Historians have suggested, for example, that the American Revolution was brought about (in part) because of a mindset among the colonists that they occupied a special place in history and had a duty to preserve it.