The Eromancer said:
Shiki doesn't just kill something like that, he ends its very existance the very concpet that gave it life is destroyed.
Close, but there's a distinct difference in meaning you're missing.
As ttestagr did, I'll try to simplify this, though I might lose some meaning in the process.
The World (i.e. the 'system' of existence of the planet Earth and everything that comes from it) has an order to it. One of the facets of order is "that which exists, does so for a reason".
There are things that support the existence of an object in the world - the "meaning" and "origin" of it, the causality that allowed it to come into being, and its compliance with the World's order.
Objects can exist as long as their conditions for existing are met. Anything that violates the rules laid down by the World's system is considered a "phantasm" - something that does not fulfill the necessary criteria for existence, and thus does not actually exist - and is mercilessly eliminated by the World.
This is logic - if something does not
exist, it cannot
be.
Everything that comes into being in the World, except its own spirits (such as the True Ancestors, i.e. Arcueid), have a predetermined end - death - built into their very concept.
What Shiki basically does when he stabs a dot on something, is basically to end all the predetermined conditions for the thing's existence in the World. Thus, moments later, the World snuffs the "killed" thing out.
(Those more knowledgeable than me, feel free to correct and/or elaborate.)
He can't kill Servants or real Noble Phantasms because they're not actually physical objects with normal origins, despite being able to affect the physical world. They're
concepts, and he can't kill those.
If he could find the Grail, he might be able to kill it, but this is doubtful since the Grail lacks a real physical form. He could definitely kill the Masters, assuming he had the ability to get close enough. Since the conditions for a Servant's ability to have a presence in the world are 1. the Grail system and 2. their link with a Master, if Shiki could end these, he could "kill" the Servant in a roundabout way - but again, he can't do the ol' dot-stab on them.
He
might be able to kill Traced Noble Phantasms, but that would be suicide, as it would cause a Broken Phantasm - all the prana loaded into the NP would explode at once, and with Shiki at ground zero, it wouldn't be a pretty sight.
As for the Soil of Genesis, it was a technique facilitated by a Reality Marble. The "enough strength to destroy a continent" thing was a comment on how much effort it would take to move it, not a description of what it actually
is.
It's really all too likely that Shiki wouldn't have been able to finish Nrvnqsr off if he hadn't morphed into his 999th Beast form, thus concentrating all those little death dots into one spot.
Remember, Nrvnqsr was mortal, too. He - like all the other DAAs, and Roa - was merely cheating death in his own way. It was costing him, too, as he had pretty much lost his identity in the process.