Well, we obviously have a difference in opinion here, and that's a good thing. A difference of opinion on a technical subject is the best way for the newbies in here to learn enough about all aspects of that subject to walk away with enough information in their head to form their own opinions. Consequently, when we find such differences in opinion, it's incumbent upon us to disagree, and publicly, so that we present our reasons, and the newbies all learn what shapes our opinions.
But, kudos to all those who walk away if this ends up turning into a name calling contest. I pledge not to go there.
1. The reason why I always remove the tank first when removing the toilet is three fold:
A) I am concerned that the stress on the porcelain at the connection might be enough to crack the porcelain of the tank or bowl.
B) When you're trying to put the toilet back onto the flange, it's like threading a needle trying to get the flange bolts through the bowl holes. Having the tank and bowl bolted together just makes that harder to do because of the extra weight you need to manuever with some degree of control.
C) A toilet is heavy and removing one will often result in a wet floor. It's awkward enough to carry a toilet bowl in a small bathroom, let alone the whole toilet. For the coupla minutes it takes to remove the tank, I'd remove the tank to get the above benefits.
2.) Certainly, if the old flange-to-bowl bolts are so short that you can't use them to set the toilet in place over the middle of the flange, then I'd replace them. However if they haven't been cut too short I don't see any need to replace them. And, that's especially true in the case of a lead bend where you'd often have to pry the lead up around the bolts to replace them.
I think the instructions here should be to replace them if necessary, but not unnecessarily.
3. I think the idea of the Tinnerman nut to hold the flange bolts vertical is a good one, but with respect, I have to disagree with MacPlumb when he says:
the reason for the the nuts and washers on the flange ... the most important reason is later down the road when you try to remove the top nuts the bolts turn and will keep from coming off.
I sincerely believe that MacPlumb's advice is a product of his own experience, but I wonder if that experience is that as he loosened the top nut and the bolt started to turn it didn't occur to him that as he loosened the top nut, the bolt would fall so that it's head would fall below the groove in the bottom of the floor flange and possibly turning in any space below the floor flange. If that happens, the fix is to pull up on the bolt while loosening the nut.
Every floor flange I've ever seen has a groove cut in the bottom of it to prevent the rectangular head of the flanget-to-bowl bolts from turning. The only way I could see them turning is if that groove was way too wide or the head of the bolt too small.
From what I can see, putting a nut and washer on before the bowl would serve primarily to prevent the bolt from falling as the top nut is loosened, but I'd be mostly concerned that there wouldn't be enough room for a nut and washer between the flange and the bowl. I kinda doubt there'd be sufficient room on my toilets, but toilets are all different that way.
4. In my view, the "caulk the joint between the bowl and the floor" idea was invented by flooring installers who wanted a way to install bathroom linoleum without removing the toilet. The problem here is that if the wax seal does leak, you won't find out about it until it's leaking downstairs and you have ceiling damage to repair.
The idea that urine and other things are going to get under the bowl and cause a big stink from all of the bacteria that'll be growing under the bowl doesn't hold water either.
Bacteria are like anything else, they need food to survive, and there isn't enough food value in soft chlorinated water to support many bacteria. Bar soap is made from vegetable oils and contains enough food to support mildew (as on bathroom walls), but we never encounter a bathroom sink overflow drain that's stinking the bathroom up, do we. In fact, those overflow drains can get so clogged up with rotting putricide that they can interfere with the sink draining properly, but they still won't stink up the bathroom.
My building has 21 toilets, and none of them are caulked to the floor. In 20years I have never had a smell coming from under a toilet bowl. Every toilet smell could be eliminated by cleaning the inside of the bowl.
Finally, what about the toilets in "women's washrooms" in commercial settings like bars and restaurants. Why caulk the toilets there? Women sit down to do that job, so they never "miss".
In my view, the risk of not knowing about a leaking wax seal is more important than the potential for bacterial growth under the toilet, and I would recommend that newbies:
a) caulk between the floor flange and the floor whenever possible, and
b) leave the bottom of the toilet uncaulked, or
c) if they choose to caulk the toilet bowl, leave it uncaulked at the back so that any water there can leak out to alert you of a problem.
5. I disagree with Redwood's advice to use a wax seal without a plastic skirt. I would use one with a skirt.
The purpose of the skirt is to prevent wax from squeezing INWARD and into the toilet drain pipe opening while you're tightening the toilet bowl down. The plastic skirt reaches down to contact the conical shape of the flange opening to form a barrier to the wax. You don't want any of that wax getting into your drain piping because it won't dissolve. It'll just help clog up your drain piping.
I know enough to know that the above are good reasons and would like to know of any better reasoning for doing thing differently. I'm still learning too.