That and Counter Guardian is not the kind of job Shiki would sign up for - he's never been interested in being a hero like Shirou was.
Shirou becoming a Counter Guardian was only incidental to his wish to become a hero. Shiki became a Counter Guardian in his own timeline (Akiha's Normal End) as part of a deal with the World to fix Akiha's Inversion Impulse, thinking he'd be able to at least live out the rest of his life with her. Then the Eclipse Epilogue happened a year or two later. Sucks to be Shiki.
I'm presuming that's part of your own setting up? Since it's not official
Yeah, gotta find some way to balance this duo out a little. As it stands now, Satsuki and Shiki are the strongest Master/Servant combo in the war aside from Dark Sakura/Black Saber (and they won't be appearing in this fic) or possibly Bazette/Lancer (which has already been nullified by Kotomine), so it's going to be a challenge to set up situations where they're sufficiently challenged by their opponent but not so much that they can't possibly win.
Shiki... hm. Shiki might be able to hit someone under Avalon, or might not. Trying to blow Avalon itself will probably pop a brain vessel, but he might be able to hit the target themselves, since he's attacking concepts rather than their actual body... would depend on the writer.
It might be better if we used the mana bomb theory in regards to the Noble Phantasms. Maybe Shiki can kill any Noble Phantasm he can hit, but destroying the NP this way would have a similar effect to using it as a Broken Phantasm, which means that Shiki can't kill any NP without effectively nuking himself and his opponent.
Second, you're forgetting that Satsuki is the most freakishly powerful mage in the Type-Moon universe, even if she doesn't have a clue what to do with it. People rising as dead apostles are about one in a million, and it takes them decades. Satsuki popped up within a day. Ciel's something like four to ten times as powerful as Rin and Sakura are (that is, normal Sakura, not 'channeling the power of a god' Sakura - though since Ciel can still pop out more power in one go, she's got pretty good odds of winning a fight if she can keep it short). Satsuki's something like four to ten times as powerful as Ciel, as far as outright magical potential goes. (That and she's essentially the third-generation descendant of Crimson Moon, so her vampiric potential is extremely high as well) If she ever starts getting a clue what she's doing, she'll be scary.
I didn't forget, that's actually part of the reason why this idea popped up in the first place. If Nasu had wanted to give any Tsukihime character a role in FSN, Satsuki would be the most natural fit on account of her enormous magical potential (...well, her or Aoko). But Sacchin actually learning to use her magic for anything other than Servant summoning would throw the balance of power completely out of whack. Given enough training, she could probably become a Sorcerer in her own right (I'm willing to bet the Sixth Magic would have something to do with violating the laws of Conservation of Energy, given what Depletion Garden does).
Avalon protects the user by creating a wall (boundary field) around him that nothing can go through,including everything Second Magic can come up with, because, as I understand, that wall completely disconnects the space it surrounds and the rest of universe,
And since Shiki can neither touch the lines through Avalon, nor kill Avalon itself, his ability is useless as long as Avalon is active.
But I agree that such details are up to the author.
I'd say Shiki could cut the lines on the boundary that Avalon creates, thereby nullifying the protection it affords. It's a moot point anyways, since it isn't likely Avalon will be making an appearance here except in its' normal role of saving Shirou from getting himself killed.
...hmm... for that matter, could Avalon have some effect on Shirou's lines while it's still in him and connected to Saber?
