So I think I'll have to copy and paste the rules I generated in SCP into the clean htaccess file from my Joomla version. I suppose by pasting it manually into the htaccess file, it won't show up in SCP as having been applied to the file.
Just an update to this thread about a workable fix:
Check your PHP Settings for your site and if it is set to use "phpfpm served by NGINX", change it to "phpfpm served by Apache". SCP works as it should, using the htaccess file.