CMYK setting

In Framemaker 2015, what does the CMYK setting do in PDF Setup, when using Press Quality?

As far as I understand, the .joboptions file is supposed to override this setting, so that the produced file is CMYK for print. But when displayed on screen, there is a substantial difference in colour between pdf files produced with CMYK and RGB. This applies too colours defined as CMYK process in FM. I want to make sure I have the right colours when the file goes to the printer.

With CMYK set, producing a pdf takes much longer, creates a smaller file and is much more likely to crash (particularly for large graphics, or if there is something non-standard in the imported graphic). Also, CMYK cannot cope with imported and rotated graphics.

I would just use the RGB setting and trust Distiller to correctly produce CMYK, but as the colour difference is significant I think I don't know how to get the right colour.