Now, I'm not going to say that the rules - including the Autofire ones - are perfect, but I agree with a few others in here that have said, basically, "Autofire that is too deadly is not fun for the players".
True, PCs that get to go around and blast NPCs that drop from one Autofire (due to houserules) are going to love it (well, most Players are). However, there is another rule that, unless you've houseruled it out, makes it just as deadly for the PCs. I think that rule's unofficial title is "What's good for the goose is good for the gander". Basically speaking, that means if the houseruled Autofire rules are more powerful against the NPCs, the same is true against the PCs.
I don't know about your games, but in mind - my players get a little sick of writing up characters because they keep getting killed, and they especially dislike being killed (easily) due to a houserule. Of course - this may just be my players. They like to invest time into building and developing their characters - often keeping journals, searching the net for pictures of their characters, etc - and, while we don't go out of our way to keep them alive (i.e. we don't make it harder to kill the PCs via houserules), we don't - at the same time - make it easier to kill NPCs.
I believe the rules, as written, were written to make the games feel more cinematic, more "Die Hard" than realistic. Of course, that's the Holy Grail, isn't it? Making a game that's realistic.....and still fun. In my experience, you can only have one or the other - and I personally perfer fun. I'll show an example of what I mean though.
"Fun" (with successful Reflex saves): As you charge across the No Man's Land between the border of South Korea and North Korea, the ground around you erupts with mortar explosions and gunfire kicking up dust behind you. With just a few scratchs from flying debris, you make it to the relative saftey of South Korea.
"Realistic" (with successful Reflex saves): As you charge across the No Man's Land between the border of South Korea and North Korea, the ground around you erupts with mortar explosions, throwing you prone from the sheer concussion. As you struggle back to your feet, the enemy's heavy machine gun opens up, and bullets tear into the ground at your feet and into your body, dropping you to a single knee. You are bleeding badly, but thankfully none of the bullets hit anything vital. As you take a quick moment of rest, to regain your bearings through the pain....a sniper's bullet penetrates your forehead, snapping your head back, killing you instantly.
Now, I'll be the first to admit that in the "Realistic" example, I assumed a few things - such as the Sniper being able to successfully make a Called Shot to the head....but then again, realistically-speaking, is it so hard to believe that a professionally-trained Sniper, firing on a target that is immobile, wouldn't be able to make that shot?
Just my thoughts on the matter. Use as you will.
Peterson