First read this thread:
Then since you are talking about patch 6431040 it is likely that the KB article doesn't apply there.
The reason is that it is a special patch. It is the only one that is in fact built up from several patches.
If you unzip it ( tar -xvf ....) then you'll find a little shell script ( install_patches.sh ) that is to be run instead of following the normal update procedure.
If you look at that script you'll notice that it does apply the normal procedure, but the script is wrapping it up. If you install the update by hand i would expect that you can still work around the down grade problem.
The shell script probably isn't prepared for the extra parameters as mentioned in the KB, so you'll either have to install the patches by hand and add the parameter there for the bundle causing the headache, or modify the script and rerun it.