This is a version 2.4.3 modification (newest versions of fckeditor have changes in paths of some files... may be don't work)
I was needed in separate folders for different textareas and rows (in example for news - images per each news item)
Warning: This is an idea only, don't apply without understanding what are u doing clearly
fckeditor.conf.php - my own config file with all lines from config.php, here (in this config) also control panel native authentication check was placed in my code
This modification takes my 4 hours... Wanna native support of runtime plugins configuration %)
Runtime configuration
oFCKeditor.Config['WA_CONFIG'] = 'f=table:field&id=ROWID';