I’ve asked this question once but made it unclear so I want to rephrase it.
I have a way of converting world position to hex coordinates. Hex map is stored as a 2D array and it’s represented on the scene via a projected green hex grid. I want to know what hex fields are ‘occupied’ by game objects on the scene.

Picture related - I’d like to know over which hexes the white box is.
This is a harder problem, and I cannot think of a perfect solution. What you could do is:
- Do a raycast or just a calculation to find the hex that contains the center of the overlaying game object.
- Recursively walk outward from the found hex and raycast upward from the center of the each adjacent hex. Note since you are checking a specific object at this point, you can do a a cheaper Collider.Raycast(), rather than a Physics.Raycast(). The walk outward is similar to a flood fill algorithm.
- If the Raycast() fails, you will need to do a check for partial coverage. Doing a Collider.Raycast() from the six corners of the hex will get most objects. Doubling it to 12 raycasts should get almost all objects. You could use a Physics.SphereCast() if you wanted extra insurance against very narrow objects, but no combination will be 100 percent sure, and performance may be an issue.