Why -flat- armor yellows in the jungle?

Because now you have +9 armor at level 1 instead of +1.21 which is better for tanking the jungle mobs at level 1, who deal almost exclusively AD for the first couple camps.

Clear times with more HP to gank with, and early surviveability

At low elo it doesn't really matter, but at high elo you may get a lot of fun to play with pre 6 and having no armor against a Leesin or Khazix would be devastating.

Scaling runes are almost always recommended over flat ones, except for for armor yellows for junglers.

Ooh, I don't know about that. Flat runes are very often recommended because an advantage over your opponent at early levels can snowball into a growing lead. It doesn't matter if you're getting an extra little bit of stats past level 7 if your opponent already has 2 kills on you by that point.

But for the jungle specifically, it's because you want to reduce the damage you take during the first few clears. You'll take extra damage if you don't have some bonus armor at the start.

Junglers with good sustain (Nunu, WW, Fidd, etc.) can get away with scaling. But most junglers need the flat armor to keep their health up. Being able to stay around full hp is necessary to gank and defend against invades.

It's to help with your first few clears. Most jungle monsters deal physical damage, so armor makes a big difference early on when you may not have the damage to finish a camp in record time. After one or two clears, you'll not really need to worry about the armor so much as you'll have your jungle item complete and will be finishing the camps much faster.

Very often if you go with armor at all, I see people suggesting armor flats. But I also see people tend to prefer scaling MR if they take any MR in their runes.

Same as above, armor flats are strong against early AA and provide good initial scaling. Scaling MR has to do with surviving endgame burst rather than early caster trades.

Someone has been messaging me recently about scaling health on their champs. The case can be made for HP over armor but scaling HP loses to armor flats in laning phase.