According to the PDF spec it's possible to create coloured annotations which are non-RGB. However, when you create i.e. a CMYK annotation, Acrobat takes the first three values and interprets them as RGB. I.e. [1 0 0 0] results in red instead of cyan, see attached example.
Interestingly, Preflight validates the document so somewhere in the company the knowledge is available.
The goal should be that annotations are displayed correctly independent of how many colour channels are there.