I had structural engineering and electronics in school and especially when you get compound units like Nm (newton meters) not wondering if the N is a newton or the SI-prefix nano is not nothing.
In the end the reason for the weird capitalization is just to avoid situations where that ambiguity will occur.
I remember me and a friend asking our physics teacher if it wasn't a problem that tera (T) and tesla (T) were the same symbol. He looked at us, paused a bit, then explained how absolutely enormous a terra tesla would be, and thus why that isn't actually an issue :P
In the end the reason for the weird capitalization is just to avoid situations where that ambiguity will occur.