[I think] that criticism applies to a few on the list but not all of them. Phrases like 'bottom line,' 'clearly,' 'essentially,' and 'basically' are often reductive or just plain filler--hardly ways of showing uncertainty or qualifying statements.
As someone who has trained a lot of regular people, some are incredibly tight, to the point that they will not be able to perform movements correctly without stretching prior to the workout. Sure, they don't stretch right off the bat--a 5-10 "active warmup" is great--but sometimes stretching before a workout is necessary. It's not like we're dealing with elite athletes here; no one on HN is going for an 800 lb squat. And even in that realm, Jim Wendler of EliteFTS.com recommends static stretching prior to workouts.
Even better than stretching or at least as good, which I don't think anyone has mentioned, is myofascial release. Basically it's a self massage with a lacrosse ball or a foam roller. Mix a little bit of this soft-tissue work into your regular stretching and you'll see huge results.
I'm not going to take the bait on the "squatting is bad for your knees" claim. There's plenty of literature and information out there that debunks this claim; maybe someone else wants to explain. . .
And sure, if you want to play sports on the weekend that's great. See how you feel. If it starts to affect your weight training, then you will have to evaluate it. If you don't care how fast you will make progress in your lifts, and you'd like to play some sports, there's obviously nothing wrong with that. Just understand that a program like Bill Starr's 5x5 is really a program for intermediate lifters, perhaps not intended for people who want to do other activities as well.
No. There's no reason to introduce long slow distance running (granted, you didn't specify the type of running, but this is usually what people mean) into your training. It will interfere with your recovery from lifting, and really won't do a lot for your overall health.
Don't you feel your heart pounding after a heavy set of five squats? I'd say that's adequate for "heart health."
If you're worried about staying "fit," you might consider adding in one conditioning day of pushing a sled or running sprints. 5x5 is a lot of volume, though, so I'd be careful with adding in anything extra.
You need to do some sort of a squat, pull, and press at least once a week. Go heavier each workout, or at least each week.
You don't need to read any fancy books about physiology, and although I think that Starting Strength is the best book on the market for learning how to train sensibly, it's no replacement for a good coach. If you go to StartingStrength.com, there is a directory of coaches. Or, just find someone at a gym who is strong, and ask him (or her) to show you a couple of lifts. Start comparing what he tells you to videos you watch online, and go from there.
Jim Wendler (of EliteFts.com) likes to say that he's glad the internet didn't exist when he was learning how to train because it forced him to go out there and just lift instead of wanking around on internet forums and trying to find the perfect 8 week program.