One of the things I like about Factorio vs other factory games like Satisfactory is that you can eventually just remove any obstacle in your path. Cliffs? Explosives. Lava? Heat-resistant platforms. It seems weird to me that you can't fill these tunnels back in, like if later down the road you need to rearrange stuff. This is effectively the only thing in the game that's permanent, and that greatly worries me when I know eventually I'll want to re-design stuff. Mod is great otherwise, I've been wondering when someone was going to make something like it.

Edit: For clarification, I'm talking about the holes leading down to different layers, not the tunnels dug out to make more space.

Good news: Apparently I'm just blind and the mod already has an item called Sealant which does exactly what I wanted it to do.

Bad news: Apparently it is also bugged, the hole is unusable but still there and cannot be built over or removed in any way.

Yes the filled hole remains but just as decorative and is meant for other things to be built over. You sure this doesnt work?

Filled hole? Is the sprite supposed to change? Because it didn't for me, it was still a hole in the ground I couldn't interact with or build over.
I'm going to remove all mods except this one and a cheat mod to test it again, I'll post results in a bit.

You need to throw the sealant into the hole until it is filled completely

Alright, I tested it again and you were right, it takes multiple sealant to fill up the hole. Great news, now if only the sprite could disappear like decorations when placing concrete or a building over it this mod would be absolutely perfect.

Edit: Just checked it out in map editor, apparently the game considers it an environmental entity, like a tree or rock. Seems like it wouldn't be hard to make it so it can be removed.