The --gen-version options is enabled per default, can't disable. This switch makes then no sense. When highlighting sources to html outlang, then following additional lines get inserted at the beginning: <pre><!-- Generator: GNU source-highlight 2.2 by Lorenzo Bettini http://www.lorenzobettini.it http://www.gnu.org/software/src-highlite --> <pre><tt> This comes from doctemplate entry /usr/share/source-highlight/ doctemplate "<!-- Generator: $additional --> <pre><tt>" "</tt></pre> " end with 2 newlines and then 2 additional newlines from expansion of $additional. I rely with my usage on exact lines in body, as in source-code. It would be reasonable enough, if just the newlines and the trailing newline gets removed. Otherwise that string is prefectly Ok. Illustration: In the Bug URL click on the function() name, you see the function context which starts/stops 4 lines too early.
Well, version 2.2 isn't in portage anymore. Besides, I think you should ask upstream for that.