Hey,

it would be awesome to get something that prevents hives & expansion boxes to not connect or have only hives & connection boxes of the same material connect

I subscribe to this suggestion. It's really tricky and can be buggy to stack hives because of this behaviour. I've raised a separate issue on a possible exploit. Having a way to specify in which direction the hive should stack would make life a lot easier. At the very least, different wood types not stacking with each other would be a good workaround.

why?

Because its messes with the way to extract/input into the hive, if all the sides of the hive are blocked

you can extract from and pipe into the expansion box

even if you could only connect to the hive, how does making the expansion box not connect help in any way?

Yes it does, because that way we can say that in a circle of 4 hives with 4 expansion boxes besides, that specific hives connect to specific expansion boxes