Hmm...good question about permanence. I wasn't thinking about removing the plugs at some point.
Miliput would be more or less permanent, as would the wood putty. That is, if you wanted to open the holes up again in the future, you'd have to dig out plugs made of either material.
White glue would not be permanent, however, because you can use hot water to dissolve it again. In modeling, there are modelers who use white glue to mask aircraft canopies for painting, because it's relatively non-reactive with the plastic material, and can be relatively easily removed.
You might not be able to immerse your scenic pieces in water, but if it won't damage them, you could drip the hot water onto the white glue plug to soften it, and use a pin or a sewing needle to insert into it and pull it out.
I don't know if that helps, this is a good technical question.
Prosit!
Bradley