Number one is a fallacy. I see people miss targets with a shotgun all the time at close range. At close quarters a shotgun payload has not had time to clear the wad and begin to expand. It's a single projectile so there is no forgiveness in shot placement. The real advantage of a shotgun is massive amounts of energy and the compounding traumatic effect of simultaneous multiple hits or a single hole that's 3/4 inch in diameter.
Number two is also a fallacy to a certain extent. The 5.56 and 5.7 rounds are excellent choices in regard to over penetration. Of course you have to pick the right bullet design for the job or overpentration is an issue with just about everything out there.
Define scope, most of the optics on these types of rifles are excellent for close quarters because of the low magnification and single plane sight acquisition. They're typically faster and easier to acquire than iron sights and they have the benefit of being used for longer ranges when necessary.
There's an old saying, it goes something like this. When you need it and don't have it you sing a different tune. Running out of ammo is never a good thing and neither is reloading and recharging a weapon on the middle of a bad situation. This is a case where more is better.
IMO if you want a black gun get an M4 variant of the AR in 5.56 with flip up tritium iron sights and stick a good ACOG on it with a weapon light underneath and be done with it. You would be very hard pressed to do better than this and you're covered in just about any scenario you can think of.
Maybe I wasn't clear, I never said it was easier to hit stuff with a shotgun than with a rifle. What I wanted to say was that When you hit a non vital part(shoulder, leg, etc) there is a lot more tissue damage than with a single bullet, making the subject a lot more incapacitated.
Given the amount of calibers, bullet designs, loads and "shooter to target distance" I guess that is a valid point if you pick the right bullet and cartridge.
In terms of scope, I was assuming that he would only use the weapon for very close combat, aka within the confines of his house/property. For that, a red dot sight would probably be sufficient. However, you're right, if he wants to shoot other stuff(as it seems like he wants to) then a proper scope is of use.
True, better to have and not need than the other way around. Although, I still stand by my original point, your primary focus should be on "How do I NOT get in such a situation" rather than "How can I fight my way out". Also, needing more than even 5 bullets to kill a threat to your life(why else would you fire?) is in my opinion inexcusably bad.
I think a M4 setup would be great, although I would have gone with a larger caliber(like 7.62 or 6.8, but that's just me). ACOG sights are great, but expensive. You'll probably spend almost as much on the ACOG as you will on a nice M4. Also, having M4's is an addiction. Once you have one, you just have to have that other one in the other caliber, barrel length, etc...
Regardless of what you get: Practice and train the hell out of it until you are an expert with your equipment. Just make sure you practice like you would fight.