Currently we have the same problem in my company: we need 2 target directories, one for the exe and one for the libraries (well, it's a bit more complex but in few words...).
After having spoken with Qt support and got the answer that it's actually not possible ("It is possible only after extracting. After extraction, you can use copy or move operation, unfortunately there is currently no other way.") I decided to use the AdminTargetDir as the second target directory. This because there's no other way to pass dynamic variables to the IFW. So after installation I call a "finalizeInstall_patch.bat" file passing the TargetDir and AdminTargetDir and this will move the libraries directory from TargetDir to AdminTargetDir. Why a .bat patch file ? because it's actually not possible to move a directory using the methods provided by the IFW. Qt support just opened a suggestion-ticket for our problem: https://bugreports.qt-project.org/browse/QTIFW-595
I hope that this answer will help others having same similar problems.
NOTE: There is a way to move a directory (on Windows), calling addOperation("Execute", "cmd /C move source dest...") but this brings to other problems out of topic here.