Could the matcher for newlispdoc be made more specific, in order to only match two semicolons at the start of a line, rather than including 3 semicolons? Here is something that should work, replacing the starts-with form on line 420, using negative look-ahead to filter out matches for more than two semi-colons:
This is important because emacs by default indents single semi-colon comments far to the right as in-line comments, and double/triple semi-colon comments to the current indentation point.