So what you need is include custom.xconfig in Pods-ios-moe.debug.xcconfig, not include Pods-ios-moe.debug.xcconfig in custom.xconfig since custom.xconfig will be reseted by libgdx during build by the code in your build.gradle:
def outFlags = file( "xcode/ios-moe/custom.xcconfig" ); outFlags.write LD_FLAGS