Besides Windows platform, pkg-config works well for both system Qt and Qt in depends.
But there are some pitfalls when using different Qt versions that are downloaded with Qt Online Installer, e.g.:
Currently, there is no way to bypass pkg-config workflow for downloaded Qt (on non-Windows platforms). I have to use a patch to bypass pkg-config on testing purpose.
It seems to be useful for developers and testers to have an additional configure option, say --with-qt-dir, which forces to bypass pkg-config workflow.
For example:
./configure --with-gui=qt5 --with-qt-dir=/home/hebasto/Qt/5.14.0/gcc_64
More refs: