OK, it was still driving me crazy, so on an entirely different VPS (using same Linux flavor and version as my Flarum site) I did a clean install using the same control panel (Hestia) -- using the built-in Hestia Quick Install button, accepting all defaults (such as using the / directory for the install (e.g., /public_html).
I ran it against Clark's website and got the same errors as on my primary site, for /vendor directory and composer files, with a D grade.
I am able to see in my browser the content of at least one file within the vendor folder, as before.
I note that the .htaccess file written by the Hestia Quick Install script properly uncommented the recommended rewrite commands.
At this point, at least I think it's not anything I did. Perhaps it is a Hestia issue (their install script), or something else.
Fortunately, yesterday after mangling my install by changing permissions and getting the white screen of death for three hours I was able to test my Hestia restore backup function and it worked like a charm.
My solution to these security concerns (which may or may not be meaningful) will be to make super-frequent offsite backups and only use that VPS for my Flarum installation.
It needs to be said that whatever Hestia has done to make Flarum install so easily was/is appreciated by me. It was the only CP that allowed for a successful import by me of a prior installation elsewhere.
My unrequested two cents on installation/importing in 2.0 would be that a script to import an existing .sql and customization of Flarum (images, extensions etc.) from somewhere and to install afresh and place it in an arbitrary directory (e.g., move an install from a /public directory and optionally be able to create it somewhere else, such as in /public_html, etc.) would be a godsend and increase non-power user confidence in not being locked into a particular VPS/server situation, especially since we don't presently seem to have any export tools to move large Flarum forums to other forum software.
All that said, I love Flarum and am amazed how well it works once installed. Thanks guys!