Here's what I came up with:
def zioUri = uri("git://github.com/scalaz/scalaz-zio.git#7f27e9cbc3")
lazy val zioJVM = ProjectRef(zioUri, "coreJVM")
lazy val zioJS = ProjectRef(zioUri, "coreJS")
lazy val base = crossProject(JSPlatform, JVMPlatform)
.jvmConfigure(_ dependsOn zioJVM)
.jsConfigure(_ dependsOn zioJS)
...
But with a bit of support here, I think it could look like
lazy val zio = CrossProjectRef(
uri("git://github.com/scalaz/scalaz-zio.git#7f27e9cbc3"),
Map(JSPlatform -> "coreJS", JVMPlatform -> "coreJVM")
)
lazy val base = crossProject(JSPlatform, JVMPlatform)
.dependsOn(zio)
...