This happened to me a few weeks ago.
I went to Colonia for the day and when I tried to come back, I had a stressful moment at Buquebus. A few years ago, I overstayed by about 30 days, and my passport is still flagged because of it. I paid the overstay fee.
I almost missed the ferry! I was literally the last person to board, just seconds before it departed. When I got to immigration, the officer looked at my passport and hesitated. Fortunately I suddenly recognized him and asked, “Do you work at EZE?” He said yes. I asked if he goes back and forth between the airport and Uruguay, and he said he does three days a week.
Then he told me he technically wasn’t supposed to let me through because exiting and re-entering would restart my 90-day period. He joked that next time I should bring him chocolates.
In the end, he let me through — but it was definitely a stressful moment. It sounds like they are cracking down on this. Even if you overstayed before and it doesn't matter where your passport is from.