That's OK, don't worry about me I'm just using you to learn the hardware
Yes, what I read is that it should give you a popup warning and once you confirmed that it "bypasses" STO and that is pretty much it. One thing that doesn't seem clear to me is whether it is possible to execute commands while the CPU is in Run Mode. The manual states that it could only be executed in PROG Mode which means no code is being executed but a couple of blogs were vague about that so I started to wonder.
But, it does look the way you suggested initially, that y8ou are doing something wrong with the parameter. Maybe just try different settings for units and motion profile.
You can conclude from the warning that commands may be executed in either case, Run or Program mode.
In program mode the program is not being executed and according to the manual:
"When the controller transitions to Program mode, the integrated safety drive is in the safe state and torque is not permitted. The controller will report Safety state = Not Running and Axis state = Start Inhibited"
And when you execute a command you get the attached warning and after clicking yes (bypass STO) then the command is executed and program code has no relevance, at the matter of fact you do not need any code at all.
On the other hand if as indicated commands may be executed in run mode then code is being executed and any code relevant to that axis has to be considered.
So if you were not getting that warning you were most likely in Run Mode.