For what it's worth, the seeker paragon feat "Primal Eye" adds their attribute bonus to their damage roll on ranged basic attacks. The current CB adds it to their at-wills that can be used as basic attacks as well (Guardian Harrier for example), which seems to me to be as close to an official stance as we're likely to get.
Character builder and its calculations is not and has never been a rules reference. Relying on its calculations as 'rules advice or official stance' has never been a good idea.
The reason 'use in place of' is different than 'counts as a' is because they... well... mean different things.
The first means the addition of an option where it did not exist before. Howling Strike is not a basic attack, you cannot use it with Commander's Strike, the only thing it does is allow you to use the power Howling Strike instead of the power Melee Basic Attack at the end of a charge. Normally you can only Melee Basic Attack at that time, so you need an exception that states 'You can use this other thing as well.' That doesn't means that other thing counts as the original thing; as an analogy if you have the option to replace your Combat Superiority with Combat Agility, that does not mean that feats that modify or require Combat Superiority necessarily work with Combat Agility. Replacement is replacement, not equivocation, in Fourth edition.
Contrast this with Eldritch Strike. This counts as a melee basic attack, that means that any time you can use a melee basic attack, you can use this power. Because it counts as one, anything that modifies the Melee Basic Attack power, also modifies this. Why? Because the power says flat out that it counts as it. This is completely different than the first case. Equivocation IS Equivocation.
The reason it works this way is because of 'Specific versus General'. If you have a game feature that changes how Basic Melee Attack works, you need a more specific rule to make that game feature affect other things. In the cast of Howling Strike, it tells you that the game feature 'charge' interacts with it, in the same manner that charge interacts with melee basic attack. It does not tell you that your handy item that boosts melee basic attack damage on a charge applies to Howling strike--it does not provide an exception to
that game feature. Eldritch Strike, on the other hand, is less targetted. It tells you that it counts as a melee basic attack, and further, it does not state any exceptions to this. That means that any game feature that refers to Melee Basic Attack is excepted by it, and thus those game features will now react to it just as they do Melee Basic Attack.
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tl;dr: Howling Strike only changes what powers the game rule 'Charge' interracts with, it does not in any way affect how weapons, or Avalanche Hammer in specific interacts with Howling Strike. Eldritch Strike changes how all game rules apply to it, and therefore DOES affect weapons, Avalanche Strike in this case.
Contrast this with a theoretical power that stated '...can be used as a melee basic attack when charging.' That means that it DOES interract with Avalanche Hammer, because it IS a melee basic attack at that time, and therefore Avalanche Hammer (and anything else modifying melee basic attacks) can interact with it freely.
