The solution is to specify to perform the qmake on the file QGLViewer/QGLViewer.pro instead of the default .pro file located in the root folder libQGLViewer-2.5.2/
ExternalProject_Add(QGLViewer
PREFIX ${CMAKE_CURRENT_BINARY_DIR}/external/qglviewer
URL ${QGLViewer_URL_REMOTE}
DOWNLOAD_DIR ${QGLViewer_DSTDIR}
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND qmake QGLViewer/QGLViewer.pro QGLVIEWER_STATIC=yes PREFIX=${CMAKE_CURRENT_BINARY_DIR}/external/qglviewer
BUILD_COMMAND make
)