For instance we may show restraint against Afghanistan insurgents in Afghanistan but if they came in through Mexico and attempted invasion in El Paso we would use totally different guidelines for engagement.  

I agree. But that's not the exercise. The exercise is based on our own government vs us. Imagine a slow turn towards communism that quickly escalated. US citizens protested in mass. That's different than an invasion of foreigners through El Paso.

It seems highly unlikely whatever remained of a US government would turn the full force against a civilian population. What would be the point? It's like $hitting in your house. Sure, you could, but then you've got nothing.

It would be a door to door style battle instead.

"They did it in Afghanistan, Somalia and dozens of other places. Why would this be any different?"

 Implementation of Use of Force models with a very large restriction on available resources.  They weren't allowed to use armor in Somalia for instance.  

 Again, asking for comparison about why we didn't do something in Afghanistan (or any country in the world) is a futile exercise unless we impose the same restrictions upon CENTCOM in the US.

You say "For this exercise, no limits......" then compare to a very limited resource environment on Foreign soil like Afghanistan.  Which is it?  Comparison to foreign engagements, or a no limits attack on the US citizen?

 Door to Door is a complete disaster.  Nobody prefers "Urban Warfare" on the invading side.  So if there are "No Limits" then door to door is not an option due to the high-resource, high-time, high-casualty rate.  

 It would make no logical sense to implement a high-casualty strategy if a low-casualty strategy is available, and approved.

 So are we talking the entire US, or a portion?

 Are we re-establishing control of physical property, or eliminating active human presence?

 Is there a time limit, or suggested time frame for the operation to succeed?

Somalia and Afghanistan were being propped up by the US, against civil unrest,... and terrorist groups.
... as usual, a sort of policing action.

In the case of a civilian uprising against our own government, well... they failed against Lincoln, and that was a much more even fight.
Imagine Lincoln having tanks and drones, tear gas, and guided missiles... fighter jets, and A10's...
The military could shut down your communications, power and water and still keep theirs.
Take away your gasoline.
The question isn't could they win,... just how much force would be needed.
US military force is virtually unlimited.

Where was that line in the Civil War?...
It was a pretty nasty business.
This time would be worse.  
US military is unimaginably stronger.
All the civilian population has is multi shooter pop guns instead of single shooter pop guns.

(Civil War had some multi shooters,... I know)...

You'd get quiet once they zipped you into the body bag...

I wouldn't expect viral agents,... chemical agents could be more selective without the danger of spread.

This really is an absurd thing to contemplate.
Going quietly or screaming like mad, makes no difference.
You lose...
This is David and Goliath in a pea gravel pit.