Hi, I'm not sure I understand your whole problem, but to confirm one part, I have successfully modified the editor in one of my installations.
The issue was that I had novice editors who were editing pages and modifying the page presentation by using the other controls like they do in MS Word, rather than just using the HTML tag selections (so a template change could not restyle the pages universally). So I modified the editor to display a default entry of "AVOID USE" for those controls (see code below) - they are still usable when required, but they can easily tell which ones to keep their hands off otherwise.
I did this in the /www/modules/fckeditor/wb_config/wb_fckconfig.js file. Note there is a default config file in one directory and this one in the wb_config one.
The editor HTML elements list is defined in this same file.
-Don
FCKConfig.DefaultFontLabel = 'AVOID USE' ;
FCKConfig.DefaultStyleLabel = 'AVOID USE' ;
FCKConfig.DefaultFontSizeLabel = 'AVOID USE' ;