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
This comes from doctemplate entry /usr/share/source-highlight/
"<!-- Generator: $additional -->
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.