I attempted a fresh install of everything on a newly brought up Arch system using the Beta 5.3.0:

http://www.mirrorservice.org/sites/download.qt-project.org/snapshots/qt/5.3/5.3.0-beta/2014-03-21_24/qt-opensource-linux-x64-android-5.3.0-beta_2014-03-21_05-03-20-21.run

.. I created a new project and from the project creation wizard I elected to setup the Android options (NDK/SDK/Java paths).

When I tried to build it, the following "General Messages" appeared:

/bin/sh: /opt/android/ndk/toolchains/arm-linux-androideabi-4.8/prebuilt/linux-x86_64/bin/arm-linux-androideabi-gcc: No such file or directory
Project ERROR: You need to set the ANDROID_NDK_ROOT environment variable to point to your Android NDK.
Could not read qmake configuration file /home/ray/Qt5.3.0/5.3/android_armv5/mkspecs/android-g++/qmake.conf.
/bin/sh: /opt/android/ndk/toolchains/arm-linux-androideabi-4.8/prebuilt/linux-x86_64/bin/arm-linux-androideabi-gcc: No such file or directory
Project ERROR: You need to set the ANDROID_NDK_ROOT environment variable to point to your Android NDK.
Could not read qmake configuration file /home/ray/Qt5.3.0/5.3/android_armv7/mkspecs/android-g++/qmake.conf.
/bin/sh: /opt/android/ndk/toolchains/x86-4.8/prebuilt/linux-x86_64/bin/i686-linux-android-gcc: No such file or directory
Project ERROR: You need to set the ANDROID_NDK_ROOT environment variable to point to your Android NDK.
Could not read qmake configuration file /home/ray/Qt5.3.0/5.3/android_x86/mkspecs/android-g++/qmake.conf.

.. the build proceeds ok, but these messages are a bit off-putting. My NDK is not in "/opt/android/ndk/", it is in /home/ray/android-ndk-r9d, and I identified this correctly in the android settings.