As a GM, I wouldn't allow an inherent stunt to discount the cost of a modular abilities gained power in exchange for losing the stunt for two reasons.
1) The On Your Toes stunt means you are very aware. Inhuman Speed means you react inhumanly quick. One is a mortal stunt, the other is a power. The two don't overlap to allow the stunt to be considered a lesser form of the power the way that Inhuman Speed is a lesser form of Supernatural Speed. One involves magic and the other does not.
2) I would rule that unless a point of refresh is a part of your modular abilities pool, then it can't interact with how you spend your modular abilities pool except in cases where the building block powers specify that a lesser form of the power is replaced . . . inhuman to supernatural, etc.
1: This is just flavor. Consider a "Faster Than I Look" stunt that has exactly the same effect; that could totally be a lesser version of the Inhuman Speed power. Similarly, just because something is a stunt in game-mechanics terms, doesn't mean it has to be nonmagical. (For a very obvious example, consider a "Hedge Wizard" lore stunt that lets you use lore as investigation for arcane matters.)
2: Not much to say here except "I disagree". If a stunt is explicitly declared as a subset of a power, I don't see any reason to prevent it from being upgraded the same way one might go from Inhuman Whatever to Supernatural Whatever. On the other hand... if it
is a subset of some power, well, there's no reason not to put that point of refresh into the modular abilities pool in the first place, is there?
That all said, I'd still look carefully at any character trying this sort of thing. I wouldn't rule it out instantly, especially for a character that was using a Human Form type limitation instead of Modular Abilities, but it's the sort of thing I'd allow on a case by case basis rather than a "yeah, this is okay for all possible characters" basis.
