Okay wait, so its best feat is basically containing an infinite-dimensional space and its Monitor-Sphere-esque "top point" (which would be the "deeper end" of the Warp) within itself.
If that's all, then it isn't killing the True Crimson King no matter how hard it tries. The large of this is due to Gan (a being who, lowballed to his absolute weakest, encompasses the Tower to the point that it's merely an infinitely small aspect of him) can't seem to kill him despite having largely the same powers as Ynnead and a few other, more devastating ones. The other large of it is that, from what I was told about it in a previous VS thread, the Warp is nothing as complex a structure as the one the Dark Tower embodies. Not only does the Tower have infinite layers; each layer in and of itself contains an infinitely-spanning multiverse, and the mere atoms of a single layer are large enough to contain the entirety of every other layer below it. Dis transcends all of this.
I also believe his regen is higher than anything Ynnead has been shown to nullify, as its best feat in this regard (from everything I've been told up to now) was destroying Slaanesh, who only has Mid-Godly. The King, being able to regenerate from the very collapse of DT reality and all of its layers, seems like his abilities would need a degree of nullification that Ynnead has not shown yet. Of course, even if I'm wrong about that,
another being who was shown to completely ignore regen on such a level was still deemed unable to get past his other defenses, so the point may be moot regardless.
The other thing is, Ynnead doesn't seem to have the degree of protection here that that the King himself does. I'm sure its powers over fate, death and concepts are potent, but I'm doubtful they're anything as strong as what Gan is capable of bringing to bear. Being the source of the very concepts of "plot" and "fate" is >>>>>>>>> merely manipulating such things (Ynn is only capable of doing so with the latter anyway), and the King is powerful enough to directly oppose Gan in those areas, having remained alive all this time as a sort of testament to that. Ynnead, as I see it, is the strongest thing in Warhammer. It has not encountered anything which can give it a true run for its money, and thus its defenses (if it has any) have not been tested against such a being.
Unless I'm missing some vital information here, the outcome of this fight is largely the same as the vast majority of fights involving the Crimson King's true form; the opponent cannot kill him, and has no means of saving themselves from his obscenely strong metahax.