In theory, LLVM might support both a very fast compilation model and a slower and more efficient one. But supporting two complete codegen backends is a lot more effort.
And overall, codegen compilation speed has never been a priority for LLVM to anywhere near the extent that it is for JS VMs. It still doesn't have parallel codegen, while all JS VMs do. That shows the very different focuses on those projects.
Actually, it can be done. It's just not the default.
It's more "nobody has had the time to erase this particular technical debt yet". Chandler, for example, is focused on erasing the debt of the old pass manager first. The B3 guys, had they focused on doing this in llvm instead of writing a new JIT + new passes + .... probably could have done that in less time.
But at this point, there are concrete plans to erase it, so as you suggest, it is highly unlikely advantages will persist in the long term :)
But this proves the overall point: B3 is able to specifically say "we are going to be faster than LLVM because we are replacing RAUW with identities, packing multiple operands into an Inst, fusing operations into macro-ops, using arrays instead of linked lists, etc." Those are specific technical decisions that the WebKit authors believe will make things faster than LLVM, and they aren't based on misunderstandings of the things that LLVM provides.
Edit: That said, there's skepticism that B3's advantages will persist in the long term. See: https://news.ycombinator.com/item?id=11107082 and http://lists.llvm.org/pipermail/llvm-dev/2016-February/09546...