I don't get it. What is weird about having every sprite be the same resolution when you want everything to be placed in a grid on the screen?
I didn't say that's weird.
It's not about C2 being smart, like any computer software C2 does what it's told to do. In this case, you're telling it to do the wrong thing.
What is wrong is having the collision polygons occupy the entire frame of the image. Those polygons are hotspots that are used to detect when the mouse is clicking the image, so if the hotspots are too big, then the click detection will be wrong.
Having overlapping images is not the issue, it's having overlapping collision polygons.
I've made two quick examples to show you the wrong and the right way to handle overlapping images. Both use identical, overlapping images.
In the wrong example, I've set the collision polygons to be the full size of the image - 256x256.
In the right example, I've set the collision polygons to fix the actual artwork in the image and not occupy the empty space around it.
Download both and tell me which one better represents the idea you're trying to achieve.