The Merriam-Webster definitions don't seem to explain a relatively new meaning.
"Pop-up" is used as an adjective to describe anything which is organized in a manner which may be border-line illegal, and it only intended to last for a short time.
A typical example would be a "pop-up shop" that is set up in a building that is temporarily empty - some of these operate literally for only a single day before closing again, to avoid any legal action. Part of the customer attraction of the concept is in actually finding out about them (via social media, etc) before they close and disappear again.
Note, "pop-up shops" are now becoming a mainstream marketing technique, and organizations are renting out space for them, etc - the original "border-line illegal" implication is starting to die out.
A similar expression for one-off events that involve a crowd of people for a short time is "flash mob." That would seem a better description of some of the protests etc in the OP's link than "pop up".