In Flexi itself, if you print and cut out of flexi, you can name your contours like you want, it doesn't matter. You just need to create it with the contour cutting tool. If wanting to differ the contours for example for kiss-cutting some contours and perforate others (if your cutter supports that), you just need to set this contours to different colours (e. g. "red" for kiss-cutting and "salmon pink" for the perforation contours will work).
When exporting data to other RIP's, the name of the cut contour DOES matter, because most of them uses spot colors with a specific name to identify contours. For example, if exporting data to an Onyx RIP, with Onyx contour cutting prefix set to default, you will have to use "CutContour" as a given Prefix to identify cut contours, and you will need to differ the contours with some letters or numbers after this prefix to differ them. For preparing data for RIP's like this, you can easily choose this specific colours from your colour palette. For example, "CutContour" for kiss-cutting and "CutContour1" for perforation will work in Onyx (even as "CutContourPerf" will do too).
So this additional cut contour colours in the standard colour palette will not do anything in Flexi, but increases compatibility to other RIP-Softwares.