It would be the time that all of the meat has reached that temp:
The stated temperature is the minimum that must be achieved and maintained in all parts of each
piece of meat for a least the stated time:
The USDA numbers don’t concern themselves with thickness or how you cook it (ie, water vs air), so it’s all about the temp of the meat.
I don’t know what makes a difference in the times. I’d say that all meat is meat and once a bit of meat is at a temp then the results are the same (at least for any given bacteria). But the USDA paper clearly disagrees. You’ll notice that they list tables for chicken with different %s of fat, starting at 25mins (1% fat) and going up to 35 mins (12%) (at 140f). They also list the salmonella numbers for beef. I was thinking that maybe fat made the difference, with fattier meats requiring longer, but similar salmonella reduction in beef is only 12 minutes. So, I don’t know. Maybe the paper goes into details. Or maybe others can explain.
FWIW, I tried searching for a PDF with the same title but for fish and couldn’t find anything.