The biggest deal with undergravel filters (the article didn't seem to go into this at great length, but I only skimmed it so I might have missed it) is that the space under the filter can get clogged with
detritus, especially in large tanks, such as yours. This can be mitigated by only using a smaller
UGF, but it will, of course, not have as great of an effect. When the space gets clogged, there are pockets of water that don't cycle. The bacteria colonies quickly use up the oxygen in these areas and die off. So far, this has been covered in the above listed article. Once you have these pockets of stagnant water, a new type of bacteria begins to thrive. These bacteria are anaerobic (don't need oxygen). Most anaerobic bacteria create waste that is really toxic. For example, botulism toxin is produced by a type of anaerobic bacteria. These ones aren't any different, and begin producing waste that is a far cry worse than anything your fish or any of the types of bacteria that are normal to a tank can make. For awhile, this will remain ok, since the area under the filter is pretty much blocked off from the rest of the tank. But eventually, something will happen that will break a little bit of detritus out, such as a thorough vacuuming of the gravel, and the toxic water seeps into the rest of the aquarium.
Now this isn't always the case. This is just the worst case scenario. However, it's one that can kill your fish with little warning.
I've got an UGF that I'm planning on getting rid of as soon as I can get the fish out of the tank for a little bit.