Wow, a lot of really good info/ideas in this thread. I also stumbled upon this article when it came out and have been experimenting with FM8/Operator and different effects since then. Didnt even know ableton had presets for formants, so thanks for pointing that out

definitely gonna spend all of tomorrow playing with that haha.
Here are some tricks that I have come across in trying to get this bass. I find good distortion is essential for getting certain formants/movement. I use Ohmicide, Tridirt and Ableton saturator. Automating the EQ between two (or even three) different distortion types creates formants and some cool timbres; and automating an extra EQ before or after the distortion can also emphasize the formant. Also, if you have a really long FX chain with a bunch of distortion/compression/EQ/etc. and place a BP or LP filter before all of them it can give you some really mean wobbly sounds. Be careful with distortion though, you can destroy a whole sound easily if you put too much.
I've also noticed that a ton of skrillex basses (especially scary monsters and scatta basses) are lacking frequencies from 450 - 650hz, which shows that he uses notching techniques like used in DnB reeces. DOA's the grid has some good tips on making cool reeces.
I feel compression also plays a big role in the sound as well. If you squash the shit out of it with a low threshold it changes the timbre and contains the beast a little bit. A trick I've been using a lot lately is putting a limiter right at the end of my FX chain (before my spectrum of course

), so it doesnt clip terribly and keeps it at a nice level while not effecting the timbre (since amplitude effects timbre with a big distortion FX chain).
As for resampling, I bet he does it but not to the extent that people think he does. I think his synths are more focused on carefully placed automation with a long FX chain and a main frequency modulation synth that has a bunch of LFO's, envelopes and automation as well. He probably bounces out after that to free up CPU and add a little extra mastering, and maybe add a sub. His signature basslines are definitely FM synthesis, and not fucking modern talking.
I've gotten really close to these synths but I dont want to post them or replicate Skrillex's for that matter. I feel its better to take these methods and do your own thing with them. One last thing is that melody is really important; thats why Skrillex got so famous is because he had these huge ass synths and combined them with beautiful 21st century chord progressions.
Hope this helps
-Rudebrat