Ernie, when I output to print at 300 dpi size as, I do not care if it flattens or not. If the file was for digital online use then RGB pdf without the X would be the one I go for.
Also from my years of experience with print and output from xara to illustrator, the CMYK colors will not be exact to the numbers in ILL. So what I do is now
export RGB from xara as pdf, take it into illustrator and readjust everything and save as illustrator file. I only do this for logos.
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