The touch driver/x configuration needs to be configured in the x startup script.
I found this to be working:
Install xinput:
sudo apt-get install xinput
then add a script call into the last line of ~/.config/lxsession/LXDE-pi/autostart
@/usr/local/bin/swapaxes.sh
The script in /usr/local/bin looks like this:
xinput set-prop 'FT5406 memory based driver' 'Evdev Axes Swap' 1
xinput set-prop 'FT5406 memory based driver' 'Evdev Axis Inversion' 0 1
This is the setting for 90° rotation. For 270° use this:
xinput set-prop 'FT5406 memory based driver' 'Evdev Axes Swap' 1
xinput set-prop 'FT5406 memory based driver' 'Evdev Axis Inversion' 1 0
The Raspberry Pi now boots into the GUI with vertical layout and working touchscreen.