There seems to be a misunderstanding. Phalanger is not platform specific. It just compiles PHP into .NET assemblies, but you do not have to use Microsoft .NET runtime engine to execute those .NET assemblies.
As I mentioned you can use Mono instead, which an Open Source implementation of .NET specification, and it runs on Linux and many other systems. Mono also supports JIT:
mono-project.com/Mono
:Runtime#Supported_Architectures
As for core developers embrace the concept of JIT, as it was mentioned in the article too, that was tried with PECL LLVM project but it has sort being abandoned for the lack of interest of more core developers to work on that. Maybe they change their minds now that many people are talking about it. The proposal is in an RFC too.
wiki.php.net/ideas/bytecodetollvm