> I don't see any way to export the site into standard html 
> pages, preserving the original extension (htm, html, 
shtml, 
> php, etc.) so that I can then work on the site and then 
> republish it to a new location.

Set Options / Spider / Check document type: Never

> I know that I am NOT going to get things like php 
scripts. 

This is the most annoying thing, indeed. 

Ah, you can also change:
Set Options / Browser ID / HTML Footer: (none)

to setup comments put inside the downloaded pages (or even 
disable this feature).