Hi, sorry for the late response.
In general users don't see or use the image based coordinates. The pixel coordinates (when there is no calibration) is aligned to the bottom-left of the pixels, not to their centers.
There are several confounding factors, in particular the way the image is painted on screen with pixel offset and bilinear interpolation. But arithmetic between pixel locations should work the same. Several functions return fractional pixel positions (zooming in, tracking, calibration).
It's hard to describe without making things even more confusing, so I'll post an image. This is a 4x4 image magnified, with the 4 center pixels colored in. I disabled pixel offset and bilinear interpolation (this could be an option if you need this for research). In yellow is Kinovea default coordinate system.
So if your image coordinates start at the top-left of the top-left pixel, then the center is at 2, 2. This is what the KVA file will store in the calibration node. If your image coordinates start at the center of the top-left pixel, then the center is at 1.5, 1.5, which is maybe what you expected.
But as mentioned this is confounded by the rendering options, pixel offset mode will make it so everything is pre-offset by half a pixel, this is relevant when the user selects locations in the image. I'm not saying this is bug-free, but the tracking work done last autumn makes me think there is no issue that would be as large as a half pixel, let me know if you find something problematic.
I think the only moment where this would be relevant is if you have an external system giving you pixel-based coordinates.