The resectioning pixel grid is relative to the pixels in the output image being evaluated. It is not inherently dependent on the image sensor's pixels/photodiodes per se.
I.e. you can have pixels with .5a sensitive area (e.g. masked phase detection photosites) and the other portion of that photosite is calculated/mathmatically replaced in the output (or the ...
I'm not familiar with camera calibration, but in any case focal length, the real focal length, does not depend on shape or size of the sensor.
Field of view does depend on shape and size of the sensor. And often we use 35mm-equivalent focal length as a measure to compare the field of view of different setups. But that's not the real focal length.
The purpose of covering the viewfinder when doing long exposures is twofold:
To prevent light entering the viewfinder from affecting metering in low light situations, particularly if there is a significant light source, such as a flashlight used by the photographer, behind the camera. For more, please see BobT's answer
To prevent light from leaking around ...
On SLR cameras, the optical path is connected to the viewfinder. Even while a picture is being taken and the mirror is up, blocking the viewfinder path, it's possible the seal/gasket between the mirror and focusing screen will let some light through. It's a very small amount of light, and usually not noticeable.
However, when taking long-exposure or bulb-...
The only reason I know of to cover the eyepiece is to keep light from throwing off the exposure meter which is built into the prism above the mirror. This is sometimes necessary when shooting from a tripod or other cases where the eye itself isn't covering the viewfinder. Canon discusses this here