I added some more options in trunk / 2.1.
But, disclaimer: the indent of the "user defined markup" is still what it was.
In trunk, you can now set priorities to base-colors too (i.e., priority for comment or string color)
If you set a user defined markup, with foreground=red, and fore-priority=1
And you change the comment and strings fore-priority to 2
then the markup will not be visible in strings/comments
Note: "will not be visible"
It is still there. The Editor still finds the match, and thinks of it as a match. But the color will be hidden, by the priority system.
If your search term has "//" in it, like "readln; // comment", and you have that text in the source, then it will color up to the //. After that it will become hidden (but still match).
If you have background color, or bold...., then you need those priors too.
Be carefully not to raise colors of comment (and other base colors) to high. If you do, then markup like highlighting the selected text, will be suppressed too.