There is a known issue with these extensions!
One of the possible marks is the alignment mark, a circle with a cross that is meant to guarantee that the color channels are properly aligned when printed. As some of you know, black text should be drawn using only black ink, so it is expected that any automatic convertion from RGB to CMYK to translate black elements into pure black ink. But these alignment marks should be painted in black, but represented by a mix of all inks: cyan, magenta, yellow, black, and possibly spot colors too, I think.
So, here we reached the real issue: if these are drawn on canvas, then there is no automatic cmyk output that will treat black text and drawing elements in a way an then treat black alignment marks diferently. So, this means that these maks should be drawn not by an extension in the document/canvas level, but by core code (in the pdf export code). And then, I agree that this functionality shoul move to the export dialog.
Juca