A1SG will respect
robots.txt, so you can set it up to block various parts for crawlers:
You can also configure
output and
analysis filters to exclude website areas.
Do also note that SMF has lots of duplicate URLs that uses canonical. While A1 Sitemap Generator will show you these URLs after website scan, the finished HTML sitemap or XML sitemap will *not* contain such URLs that through canonical meta tag refer to another "master" URL. (This can explain the difference you see.)
I believe hat next version of A1 Sitemap Generator will contain a website scan "preset" for SMF. (Will probably default to leaving out e.g. profile pages etc.)