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If we have enabled option: and then toggle option: then we indeed see the prompt "Some comparison options have changed. Would you like to re-compare now?" as it should be.
However, if we put the latter option (about spaces) to the customized toolbar and toggle it from there, then the re-compare procedure starts without any prompt.
Is this the designed behaviour?

ExamDiff Pro v12.0.1.8 (64 bits).

Yes. When you use the toolbar, it's effectively a command, and it consists of changing the respective option and recomparing.

That seems strange to me. Finding one's way into Options and navigating the options tree to locate a specific option is such a deliberate process that it's hard to see how one could do it accidentally ... so the warning then is unlikely to be needed - unless of course one changed the 'wrong' option.

But clicking a toolbar icon, perhaps the 'wrong' one, is a whole lot easier to do and it's just a single click. I'd have thought a user might more reasonably want the warning in that case.

It's not about safety of an option change, after all the change can be easily undone. The toolbar command is simply a shortcut, a one-click action, normally expected from toolbars. Think of it not as an option change but as "Recompare with a different option".