I would think that the page should default to having all of the checkboxes checked, with a javascript button for unselecting all.

I would also think that the "Ignore Inline" option would make the most sense not by ignoring the inline code completely, but by having box for inlinve code not checked by default.

Either way, having some sort of visual cue in the table rows for inlined code might be handy for people in some nodes that are very full of code, as a reminder of why that one random snippet is in it's own section.

These are of course just my opinions, I don't presume everyone thinks the way i do, but it's something you might wnat to consider.