So how does Ezuri, Claw of Progress interact with a Fractal that starts with more than 2 +1/+1 counters?
I would guess that the fractal gets the counters on arrival and therefore doesn't trigger Ezuri.
Indeed, Ezuri's first ability doesn't trigger if an otherwise 0/0 creature enters the battlefield with three or more +1/+1 counters. This is because—
that ability is an enters-the battlefield ability that checks the state of the game immediately after the creature enters the battlefield (C.R. 603.6a, 603.10), and
the +1/+1 counters start changing the creature's power and toughness from the moment the creature enters the battlefield; the creature doesn't enter as 0/0 and then change to a different power and toughness (C.R. 603.5, 613.1g, 613.4c; see also C.R. 603.6c, 611.3c).