Would you allow that with a makeup kit plus this feat? I wouldn't unless the player could describe to me, in game, how his disguise worked. And if the explanation made sense I'd probably allow it with or without the feat. The feat doesn't seem to add value.
Ugh, I hate that attitude. I had DMs that would pull this all the time - it doesn't matter how good my character might be at disarming traps, if
I personally could not explain how I was disabling it - and somehow predict, despite not being a thief/rogue myself, how to bypass the dangers of the trap, it would go off in my face.
I'm not a 7th level Rogue. I'm not trained in disarming traps, or opening locks, or most of my character's skills. One doesn't require the Fighter to prove they can lift weights and swing a sword in order for their character to do so - one should not require similar ability for a character to make use of their skills. I understand why you would want that, but I think it can be really unfair to certain characters to tie their capabilities to those of the player, while not doing so for others.
The point of these abilities is that they are the height of talent, and demonstrations of capability that are within human ability, but so far beyond the default as to be out of reach of most people.
They shouldn't conflict with normal skill use, because they are taking things to another level. A character can still use basic disguise and forgery on their own, in the normal means - these just provide some additional methods that will generally be more effective for those who have invested the time and effort in mastering and using them.
My group knows a ritual that lets us magically learn the rumors circulating through a city - that doesn't render Streetwise meaningless, it just gives us another way to gather information in the right circumstances. (Like, recently, when the entire party found ourselves in an eladrin city in the Feywild - as obvious outsiders, asking certain questions around town would have tipped people off about our interest, but staying in our room and performing the ritual avoided that problem. In a normal city, on the other hand, we probably wouldn't bother.)
I don't think these abilities will override normal skill use any more than similar rituals do - both are simply other tools in a character's arsenal. Now, I could be wrong - we haven't seen them all, yet. But I'd be really surprised if we see some that completely render normal skill use null and void.
I am eager to see the crafting stuff - I like the idea that some epic craftsman can forge a legendary blade simply through his own skill, rather than needing to also be a spellcaster.