No, that isn't it, re-read the article. The illusion is supposed to be that three flashes that are not evenly spaced, or are even spaced out of order (1--3-2) get perceived by the brain as evenly-spaced an in order.
Look at the explanatory diagram with the labels "What our eyes see" and "What our brain "sees"" (the third image on the page).
The gif is just broken. It's supposed to have a space between the second and third flashes.
Yes I see the last one was supposed to flash twice, but at 2 positions. The explanation is the same though as far as I understood the article, that the brain processes all flashes as a single temporal chunk and that is what causes the temporal re-alignment. It kind of resembles the famous letter-jumbling where you can still read the text if you re-arrange the letters inside the words if you read fast enough.
Look at the explanatory diagram with the labels "What our eyes see" and "What our brain "sees"" (the third image on the page).
The gif is just broken. It's supposed to have a space between the second and third flashes.