OK, the problem here is people confuse RF noise with audio whine caused by the alternator.
The whine you are getting is NOT RF (Radio Frequency) noise at all. RF Protection will not help at all.
You are hearing the AUDIO frequency variations from the alternator riding on the power lead.
The best way to get rid of this is to take power directly from the battery. You still need to have a fuse, and it should be mounted as close to the battery as practical.
If you also get the ground from the battery directly, this lead needs a fuse also.
If you still have the whine, then you need to add an "Alternator Whine" filter. This is large choke (not to be confused with small ferrite beads used for RF filtering). The "Secondary of the transformer" trick is just using the transformer winding as the choke.
The twisting the power wires is mostly for RF protection. It will also help with STRONG electromagnetic low frequency fields like 60 Hz around AC power equipment. The whine you are hearing is NOT a strong enough field to be picked up this way, so while it is a good general practice will not address your problem.
I hope this helps clear up some of the misconceptions people have.