"For those that are "well prepared", how do you deal with the rifle-equipped bad guy at the tree line who will turn your head into a pink cloud when you walk to your wood pile? Everything you've amassed is now his."

Good point.
I am one of the well prepared people, high on a mountain in North Carolina with lots of food, water, firewood, and guns.
You can't see my house from the road, or from any other house. I am 3/4 miles up a private gravel road, there are 4 other houses on this road.

In the event that the S hits the F we would certainly have some bad guys out there who would want to kill people and take their stuff.
Of the other four houses up on my mountain, I doubt that any of them have anything put away for a disaster.
Three of those houses are uninhabited and people just come up there for holidays etc.
My brother lives in the other house with his son.

I know my brother has done nothing to prepare.
So I would probably get my brother and his son to move in at my place. That way we would have 3 men and 2 females. Everybody would have a gun, or two.

First, the bad guy has to figure out that my house even exists. Then, he has to figure out that we have stuff that he wants.
Then, as you say, he has to hide in the woods and blow someone's head off.
Well and good, but he still has to kill 4 other people.

This is reason number one why I have told nobody about my stockpiles, not even my brother. Nobody knows I got anything and hopefully they will leave me alone.

If a couple of bad ass guys figure out what a honey hole my house is, they hide in the woods and stage a proper ambush and kill my brother and me at once, then they would take the place. Not too likely to happen, but it could happen.

I have taken the reasonable steps to set myself up to give it a good fight. If I get killed 30 days after the EMP, well tough luck. At least I would get my name in the paper.

Oops, forget that, there would be no newspapers.