qmake generates Makefile according to mkspecs, gcc does linking according to instruction in Makefile, inspect Makefile to verify that linking instructions are correct.
As far as I know binaries does not contain path to linked libraries, only library names, so only way for ldd to know exact path is to look for libraries in $PATH variable, which means that ldd can lie to you if $PATH during compilation is different from the $PATH during executing ldd.
Another way to put it: when ldd says app is linked to libQt6Widgets.so.6 - it is a fact, but when it says libQt6Widgets.so.6 is /lib/x86_64-linux-gnu/libQt6Widgets.so.6 - it's a guess.