No need to use the stomp slot if you are using a recent release firmware. Go into Rig menu and set it there.
There will always be a slight latency but not one I find too noticeable within 1-2 steps.
Make sure you are not hearing the natural acoustic sound of the guitar strings over top over the transpose, as that would make things worse. So play louder or wear headphones.
Thank you. I am not on the latest firmware, so I am going to try updating, maybe it allready brings an improvement. Any remarks on using Transpose effect on clean Tone, never had any problems?