I have a "Quake 4 Shortcuts" folder, where I placed three shortcuts that I created from the quake4.exe (via r-click-->Create Shortcut). For each shortcut, I added different things to the "target" field (after the path to Quake4.exe).
Play: H:\Quake4\Quake4.exe +seta com_allowConsole 1 +disconnect +exec pjw.cfg
Test: H:\Quake4\Quake4.exe +seta com_allowConsole 1 +disconnect +exec maptest.cfg
Edit: H:\Quake4\Quake4.exe +r_brightness 1 +r_fullscreen 0 +editor
As long as you have your tweaked settings saved off to a separate config (and not just in Quake4Config.cfg), then you should be able to open up Quake 4 and go to Settings-->Load Defaults, and the editor should run okay with the above command line and default settings.
My pjw.cfg is just my standard play config w. key bindings, etc. (If you want to be entertained by my weird config, you can exec pjw.cfg, since it shipped with the game.

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My maptest.cfg is:
seta si_pure "0"
seta net_allowcheats "1"
seta net_lanserver "1"
seta si_map "mp/pjw4tourney1"
spawnserver
so when it's exec'ed, it just automatically creates a server running whatever map you're working on and drops you into it. Saves a few clicks--especially when you're loading it up a lot and tweaking things...you could either add a line to that that loads your tweaked config, or else just change the default key bindings as needed, so you'll know what it looks like for others, or even make two different "Test" shortcuts, one with +exec a1yssa_l33t.cfg and one without.
Hope this helps!
VVVV Good addition Mazor, thanks!