the 3D Benchy isn't a specific calibration test
With the Benchy you don't see if your printer is calibrated in any axis, but it is a general use-case test for a model that can show you many of the issues you might face in a normal print. For all intents and purposes, it is more a general Benchmark item than a specific calibration test like a cube, stringing test, or temperature tower, where you go through iterations of a profile to dial in settings and printer properties.
the 3D Benchy is a Benchmark for printer and settings
Most of the printing issues that can be seen on a Benchy are related to the print settings, though some are also related to the physical properties.
The bow of the Benchy has a shape that is very conducive to seeing how much the printer can handle overhangs due to proper cooling and settings.
The arches in the sides of the cabin, as well as the back window, have a rather challenging overhang pattern (the extension needs to be larger and larger), and the front of the Benchy has a short bridge, which shows if cooling is happening properly.
The upper edge of the hull also is a little overhang, which shows how well small oversteps can be printed.
The funnel of the Benchy is of sufficient small crossection, that with bad settings it can result in printing layers upon one another too fast, which can result in bulging, misinformation, or totally blobing that area.
The front and back corners are rather sharp and can show the effects of ringing on the area next to them due to bad acceleration settings