The "solution" often is:

every web site is different.

In general you write a unique script for each one. Sites based on a similar
template, could probably utilize a pre-existing script done for that site,
with maybe minor customization.

I was hoping there are advanced features of HTTrack that I'm not aware of that
take this into consideration.

But tell you what: what specific website are you looking at ? I'd have to look
at it and see how it's put together, before I can speak in terms of a real
script.

From what I've done with automation, most sites are doable, once you know how
they work.

The other side of the problem is the user's PC. I've had scripts run like
clockwork on mine, then the customer's PC or MSIE is just a disaster. I
remember revising one script so heavily that eventually I dropped the
customer, because it just wasn't worth it.