manually-preload-with-cron-jobs

If I setup a Cron job as per https://www.wpfastestcache.com/features/manually-preload-with-cron-jobs/, will this rebuild the Cache on the entire site, or just those pages marked to build the cache automatically and preload being active?

yes.

I have noticed that on some low traffic sites, some lesser visited pages are not being cached until visited, unlike say the homepage.

yes, you are right so we added this feature.

Sorry, if I setup Preload and run the script, do I still need to mark pages to build the cache automatically as well?

yes, the preload option must be enabled.