@Mican, I bet this is what you're talking about. If you create a 'sensitive text' input variable from the Variables panel (as opposed to from an action, where 'sensitive text' isn't an option), e.g.

your flow will run fine from the editor and (presumably) load the variable with whatever you set for a default value (no popup). But when you run it from the Flows panel, you get a popup.
Seems likely that creating an 'Input' variable from the Variables panel (which has no dialog options other than content, nothing other than variable name to let the user know what's desired) means that a default dialog will be created, i.e. the message, just because it's an 'input' variable.
The types we can create from the Variables panel are limited to 'input' and 'output', so we're stuck, I guess.
But there ought to be a way to create a Flow variable as 'sensitive text' (ergo with no offending popup).

It's either a bug or a "feature."
I think creation of an input variable should get some added attributes/parameters (like those of the Flow action for input dialogs). Plus we should have the ability to create a 'sensitive text' variable from the Actions that won't pop up a dialog at all, regardless of how the flow is run.