The way I look at it is that that you need to threaten a target to gain your bonus.
Melee attack and threaten are interchangeable, with the noted exceptions... it's just an easier way to look at the situation, since that is the way threaten is written.
You're confusing the rules again. This is a generalization that doesn't hold true. We -- even you have pointed out a few -- have shown cases where you can make a melee attack without threatening. Melee attack and threaten are NOT interchangeable, BECAUSE of the noted exceptions. The exceptions negate the rule you're trying to establish. Take a look at this statement, which uses the same logic:
"All puppies are brown, with the noted exceptions."
See how ludicrous that statement is? If you can find one puppy which is NOT brown you've invalidated the first part of the statement, and the second part is completely superfluous and makes the whole thing nonsensical.
By strict definition, to gain a flank bonus you must be able to melee attack your target ...
I'm with you, assuming the other conditions are also met.
... and by default, you must threaten your target.
Why do you continue to cling to this? It's a generalization that is just plain wrong. And it's the source of a lot fo confusion.
These situations are fairly rare, and infact, since 3.0 and 3.5 have come out, to date, no one has used a whip in my games.
It's not rare to the character build that uses a whip. Or a non-improved unarmed strike with a gauntlet. Just because you've not seen it used in a game doesn't establish a statistical fact.
It is just easier to use the word threaten when explaining the game to novice players and DM's, since most of them wont face this situation very often.
Again, threaten and melee attack are 2 different things, but one and the same in most cases
This shorthand generalization you're using is wrong, and it's just going to confuse players later on. It is much more beneficial to tell them what the rules actually say. There's a lot of inconsistencies in your posts, and I think it's because you're confusing making a melee attack and threatening.
Edit: I get what you're trying to say, and I agree that in some cases it holds true. But it does not hold true in all cases -- as in the examples used previously -- so you can't claim it establishes a rule that you have to threaten in order to flank.