Rob,
If I go to 'InDesign preferences', then these are (in my mind and the minds of many many others) the preferences for the software, not a document.
If units are document based, their preferences should not be within 'InDesign Preferences'. That's pure logic.
I agree that units have no influence on output but it is just a practical issue. One that is very annoying when you have to re-set to mm each time you get a US document. In a high-speed graphic agency where short deadlines are crucial, the last thing you want to do is put time in changing your preferences constantly. The whole point of preferences are so that you don't have to think about these things anymore, and so that you don't have to first scan your interface for unwanted changed settings.
So no, it has no affect on output but on work-efficiency, and that is not to be neglected neither.
It is also not a massive problem, just an annoying thing that I just think they can do better... A warning of units could then help to remind you that settings have been changed instead of finding out along the way. But I do think it is a nice thing to have AdobeCC say something like: "the document you are trying to open has different units than your preferences, do you want to keep them? yes/no" It's just a simpler more user-friendly approach.
But hey, that's just me:-)