There are no options for ignoring sections when using command XML Convert to CR/LFs.
You can only write a script or macro which protects the format of such a section for example by replacing every space inside such a section by a non breaking space (decimal code 160, hexadecimal code A0), every line termination inside such a section by another special character like the paragraph character (decimal code 182, hex. B6), and every tab character for example by the character with decimal code 187 which results in converting those sections into single line with no whitespace characters inside. After executing XML Convert to CR/LFs also from within the macro/script, the macro/script replaces the non breaking spaces back to normal spaces, the paragraph characters back to line terminations and the » characters back to tabs.
It is not really difficult to code this with a macro or script. I just can't do that now because I don't have input examples for the macro/script. Of course that method with converting a CDATA section temporarily into a non-breakable single line string could fail when such CDATA sections have in total more than 20.000 characters. However, also in this case I would have already an idea how to solve this, but if that idea works depends on the sources which I don't have.