Yes, the two should be completly seperate.. What my idea is like is that you have one big admin script(the portal i guess) then you have the mods,plugins, scripts(BB, news, BUG sytems, FAQ systems, shopping cart system) and all these could be removed, added, updated, and used through this admincenter(portal). Ranking sytems for the site "team" would be setup to where once you added a certin plugin, mod, or script that needed to use the raning system(almost all) you could add it to that certin user..
Admin - can do anything
Moderator 1 - News poster(only if news plugin/script/mod is installed)
Moderator 2 - Forum moderator(only if that plugin/script/mod is installed)
Moderator 3 - News poster, Forum moderator(only if those two plugins/scripts/mods are installed)
and so on... you get the idea.. the main admincenter would have no effect on the site design except for providing the services.. our sites shouldnt have to bend over for the script, it should bend over for the site.. so we make the scripts look like our site, not our site look like the script