This sounds exactly like what I needed to hear. I was having a difficult time wrapping my head around this issue.
To confirm that I have it understood, can you answer this for me please:
To make my app work, I'd be building the app as if it were stand-alone, but using the WordPress API and WP's coding best practices?
For example:
// Store table name in variable before creating it
$table_name = $wpdb->prefix . "cannedcomments";