In JavaScript, what is event.isTrigger?

In jQuery 1.7.2 (unminified) line 3148 contains event.isTrigger = true; nested within the trigger function. So yes, you are correct - this is only flagged when you use .trigger() and is used internally to determine how to handle events.

If you look at jQuery github project, inside trigger.js file line 49 (link here) you can find how isTrigger gets calculated.

If you add a trigger in your JavaScript and debug through, You can see how the breakpoint reaches this codeline (checked in jQuery-2.1.3.js for this SO question)

Modern browsers fight against popup windows opened by automated scripts, not real users clicks. If you don't mind promptly opening and closing a window for a real user click and showing a blocked popup window warning for an automated click then you may use this way:

button.onclick = (ev) => {

  // Window will be shortly shown and closed for a real user click.
  // For automated clicks a blocked popup warning will be shown.
  const w = window.open();
  if (w) {
    w.close();
    console.log('Real user clicked the button.');
    return;
  }
  console.log('Automated click detected.');
};