@Misaki All zero length bones (all the bone icons) behave the same. The icon does not affect mouse selection. Also the zoom level, which affects the size of the icon, does not affect mouse selection, it remains a fixed distance from the bone.
When you have 2 bones exactly on top of each other, the very center of one of the bones works differently for selection. This is done to allow for selecting a bone even when another bone crosses it's center. If you move slightly farther out from the center, then you'll be able to select the other bone.
When you have 3 or more bones exactly on top of each other, you'll only be able to hit 2 of them: the center of the one on top, and a little farther out you'll hit one of the other bones. I agree this can be inconvenient.
One current option is to enable the name tag for the 3rd bone that can't be hit. You can click the name tag to select.
The bone icons aren't a bad idea, but it requires knowing about the problem and that those bone icons solve it. It would be nice to have a solution that didn't require special bone icons. We could detect bones on top of each other and make the hit detection circle like a pie, where each bone gets a percentage. You'd not intuitively know where to move the mouse to select a bone, but at least it would be possible (you see the name of the bone you are over before you click). Or maybe instead of the pie just have more "rings" of hit detection, so all the bones can be hit.
Some apps show a popup menu to choose which to select. This is OK, though reading a list tends to not be very fast. We've considered adding it, for bones and attachments.
