I always like to lead in a new site/scan with a Crawl-Only. This
often exposes issues with the current settings. Since it takes less
time than a full audit, I can make the necessary modifications before
running a fresh scan. It also will show external links or
sub-areas that I may not want to scan at this time. Being a
Crawl-Only, I can deselect those branches from the site tree before
continuing with the Audit.
As for the template idea,
I always save the Crawl-Only as its own SPA file. I then continue
with the Audit phase(s). If the Audit goes awry, I can run a
different Audit with a customized policy using the orginal Crawl-Only
SPA file. For larger sites, I may end up with two or more "Audits", but
will be able to combine them into a single Report.