This task refers to the recommended developer setup using qt5.git with submodules.
Running configure in a tree where configure was previously run does not reconfigure any module except qtbase. This behaviour is not very intuitive and causes much confusion for users – you rerun configure to change some option and you get a broken repo (and probably a failed build) where qtbase has your new configure options and the other modules keep the options from the first configure run.
There appears to be no obvious way to force configure to reconfigure the other modules from the top-level, one must "make qmake" in each submodule – and very few users will even think of doing that. Even deleting the .qmake.cache in each submodule doesn't cause configure to be rerun for that module.
For usability, configure must behave consistently, regardless of whether its the first run or a later run, otherwise users will be forced to waste a lot of time doing a clean build from a fresh copy of the tree every time.