> How can I tell HTTrack to just leave these relative links
> alone?  (BTW, I don't use any <base> tags.)

You can't - httrack will always rewrite links downloaded in 
relative form, or rewrite links not downloaded in absolute 
form by default. You can disable the rewriting system, but 
no links will be rewritten in this case (see Build options)

You may, however, post-process downloaded html files and 
replace the desired links, using some Unix-bash-scripting 
function.