Nope. It is simply that the unmodified damage value is used to when attacking the opponent. That's why Perplex and the like can't be used (since they would modify the combat value... which, per the feat, can't be modified). The timing really doesn't have anything at all to do with it.

I am not sure what you are getting at here, other than providing rules lawyers with fodder

Of course it doesn't allow these because the rules superceded are the ones specifically listed on the card
The cards also do not say that you cannot give your opponent a slap upside the head when they use Alt FF either

Stunning Blow: When the character makes a successful attack with Incapacitate, in addition to the effects of Incapacitate, the character may deal damage equal to its unmodified damage value. The attacker may choose how to divide damage dealt among the successfully hit targets.

INCAPACITATE (OPTIONAL): Give this character a close combat action or ranged combat action; its damage value becomes 0 until the action has been resolved. If this character successfully hits a target that has zero or one action token, give the target an action token.

So technically, Stunning Blow does absolutely nothing. According to the phrasing, the character does damage equal to 0
Phrasing closer to Nova Blast (something like 'When the character uses Incapacitate it does not reduce it’s damage to 0, but uses its unmodified damage value') would be better
But that does not change the fact of the intent

The intent is that you can deal your normal base damage value, unmodified by any powers, abilities or team abilities when you hit with Incapacitate

If anyone ever tried to argue otherwise with me at an event I would consider that to be the poorest sportsmanship I have EVER seen and I would be hard pressed not to DQ them on the spot for being a dink

This kind of begs the question if people know that this is the intent and play it that way, then why does the Super Strength arguement change the usage of Pounce? If Pounce were altered because of a change in the power as a by-product (ie. Pounce wasn't specifically targetted for the nerf), why can't you go by the "intent" for it?