I've never tried it, but how about this:

Rather than pointing httrack at the remote website, point 
it at your local copy, and get it to create another mirror 
of the local copy, using the different settings you want?
I guess this relies on httrack being 'dumb' enough not to 
realise you're asking it to mirror one of its own mirrors!  
But it's clever software and may try and prevent you doing 
this, I don't know.

You may have to play around with your local web server 
settings, so that your local copy of the remote website 
looks (to httrack) like a proper website, and not just a 
bunch of local files.