Both keyboards are great, I use an Advantage LF at work, and for the last several weeks an Ergodox at home.
My main issue with the Ergodox is I misstype keys, especially the number row. I never misstype on the Advantage, but on the Ergodox I have to peek at the keyboard occasionally.
Programmability wise, the Ergodox is more flexible, but you have to go to the website, then (for me) compile the firmware, flash the keyboard, etc, while with the Advantage you do it on the keyboard itself literally in few seconds. So there are pros and cons in each case.
Regarding the layer switch key on the Advantage, it CAN be remapped, however you need a footswitch to do so:
Go to remap mode, hit the footswitch as the "source" and then hit the destination key you want to clone the function to.
The key becomes a remap toggler. In my case I prefer a momentary layer shifter, which is how only the footswitch operates, but I solved that by adding extra keys that I wired to the footswitch terminals. You can read about my mods here:
http://geekhack.org/index.php?topic=26579.0