Cross compilation, pkg-config issue

I am trying to cross compile Qt-5.9 for an ARM target using the latest ptxdist (2017.06.0) and OSELAS toolchain (2016.06.1).

The problem I encounter is related to Qt requiring the environment variable PKG_CONFIG_SYSROOT_DIR which is somewhat not a good idea:
In my understanding, this variable is owned by pkg-config itself. Since the qt-configuration requires it and exports it at the same time.

1) when trying to configure Qt without -pkg-config, as one would expect, it will not pass the config-tests for dbus and a bunch of other libraries, due to not finding the corresponding headers.

2) when trying to configure Qt with -pkg-config, the configuration is disabling pkg-config again, thus not passing config-tests. The reason is printed by configure as follows:

WARNING: Disabling pkg-config since PKG_CONFIG_SYSROOT_DIR is not set.
Set this variable to your sysroot for pkg-config to function correctly when
cross-compiling or use -pkg-config to override this test.

3) when trying to configure Qt with -pkg-config and supplying the environment variable PKG_CONFIG_SYSROOT_DIR accordingly, the config-test for dbus (unexpectedly) still fails.

After some research, I could locate the problem to the call of pkg-config, excerpt from config.log (shortened to the relevant bits):

pkg-config --cflags dbus-1 '>=' 1.2
> -I/home/<lengthy-path-to-sysroot>/home/<lengthy-path-to-sysroot>/usr/include/dbus-1.0 -I/home/<lengthy-path-to-sysroot>/home/<lengthy-path-to-sysroot>/usr/lib/dbus-1.0/include 

Apparently pkg-config prepends the actual include path once again with the path to the SYSROOT, picked up from PKG_CONFIG_SYSROOT_DIR. pkg-config(1) reveals the reason for that:

       PKG_CONFIG_SYSROOT_DIR
              Modify  -I and -L to use the directories located in target sysroot.  this option is useful when cross-compiling packages that use pkg-config to determine CFLAGS and LDFLAGS. -I and -L are modi‐
              fied to point to the new system root. this means that a -I/usr/include/libfoo will become -I/var/target/usr/include/libfoo with a PKG_CONFIG_SYSROOT_DIR equal to /var/target (same rule apply to
              -L)

As a solution to that, the Qt configuration should either:
1) Not require pkg-configs variables to be configured
2) Require them but not export them.

As a workaround, I decided to choose 1), which I absolutely consider a workaround, not a proper fix (see attached patch).

On the other hand, I can hardly believe that I am the first one running into this issue with cross-compilation, so if I made blatantly wrong assumptions about how to cross-compile Qt5.9 I'd be glad to be enlightened.