They should not be doing those things, as they are meant to always be hidden from the player.

Thanks for report!

Fixed!

They can still take damage through scripted events. can you make them immune to repair, and give them regeneration?

It has already the flags:

    flags = {
        "placeable-neutral", 
        "player-creation", 
        "fast-replaceable-no-build-while-moving",
        "placeable-off-grid",
        "not-on-map",
        "not-blueprintable",
        "not-deconstructable",
        "not-selectable-in-game"
    },

What I need to add?
https://wiki.factorio.com/Types/EntityPrototypeFlags

So, please check the version 1.0.4

https://wiki.factorio.com/Types/EntityPrototypeFlags#.22not-repairable.22

not-repairable is a flag for rocks and trees: You can damage them, but not repair.