qmake is not arm64 when building from source for arm64

I'm building from source because I need a universal build. The build machine is an Intel Mac.  I put more details under Environment.

I added to configure as described here: https://www.qt.io/blog/qt-on-apple-silicon

When testing I tried building only for arm64, which is why my current config is a follows. But I got the same result when building for both as described in the blog. 

../Src/configure -prefix $PWD/Qt6.2.0-beta4/ -skip qt3d -skip qtactiveqt -skip qtlocation -skip qtmultimedia -skip qtserialport -skip qtquickcontrols -skip qtsensors -nomake tests -nomake examples -skip qtcharts -DCMAKE_OSX_ARCHITECTURES="arm64"

I use ninja to build. Followed by ninja install. 

When I check the architecture of the qmake file in the prefix folder using lipo, it's x86_64.

The project which is using Qt is still built using qmake, which is why I'm checking that file.

Is there some step that I'm missing to get this to work?