Right now, libuv will **always** be built for the host system (at least when building on OSX) because the information about the cross compiler is never actually passed to GYP. I don't know how anybody has been managing to build cross compilers with this.
Note that, at least on OSX, there is a bug in GYP that will send clang flags to non-clang compilers and it will still attempt to use Xcode's libtool, so this doesn't completely fix the problem of cross-compiling on an OSX host, but it's a start.