That also means it's effectively encouraging asm.js adoption, which might give Apple and Microsoft enough of a kick to optimize that. Google seem to already be planning on it (they added some asm.js tests to their Octane benchmark).
It also might be useful if, at some point, other browsers want to implement a PNaCl runtime. One of the main sticking points (aside from the use of LLVM bitcode, which is not something LLVM was designed for) was that it requires the Pepper API, which is huge, and duplicates much of the existing web APIs. Google have the spare engineers to do that, but Mozilla certainly doesn't.
A reverse of that would be useful too - an implementation of the standard web APIs on top of Pepper, so you could re-target an asm.js app to PNaCl. Or some kind of tooling that lets you transparently target both.
Maybe we'll see some kind of convergence thing going on? Wouldn't surprise me too much if they started evolving slightly towards one another. I think it's probable that asm.js will eventually get some kind of compact bytecode representation, especially if it can be implemented as a shim to allow it to load in existing browsers.