Ok, I can reliably reproduce the fault.Attached is the config I'm using. To get the debug messages you gotta run it from the terminal.linuxcnc path/to/config/tool-sensor-test.ini
You can trigger the tool touch probe on the right side panel (Probing is active when the feed rate is 5, aka slow

)
If you start the config for the first time there are no linuxcnc.var and linuxcnc.var.bak files in the config directory. I think this is where the issue comes into play.
On this first start look at the program movement from the Y perspective and you will see it will exceed Z axis limit.
If you set the G54 origin (Nullpunkt) to -5 the program will fit into the machine.
Now you can measure the tool height with "T1 M6" in MDI and use the "Sensor Trigger" button to make a measurement. (Remember it probes twice, so click wait a second and click again

)
After measurement you can play the program without warning message. If you check the Y-perspective again you can see it's at the bottom of the machine now.
Now go to G54 X0 Y0 Z5 and do a touch of again. This would set the G54 origin at machine X0Y0Z0 before any tool measurement and this makes the program run out of the machine boundaries. But the preview shows that the program is perfectly fine inside the machine boundaries.
Now I'm not sure how to get rid of this warning yet but I thought if you and I can reproduce the issue with the same setup we can find a solution soon
I am in the IRC channel if you want to have a quicker back and forth chat on how to fix this issue.