I think most MODs can be undone, but some, like stickers might not do so well to take them off. I put on the bookcase sticker set and I love it, and you could probably get it off, just not sure on that to be honest.
Otherwise most mod's, that I put on at least, are reversible. I put in Uncle Lester in the chair and he can easily come out if you wanted. I also did a lot of light mods and those were all just clip on mods, so again, they can easily come back off.
I did change my flipper buttons to be clear with a blue LED on them and those I had to screw in on the inside of the cabinet, you could back those out and put in the originals, but the small screw holes inside would be left.
I can't think of any MODs that are permanent off hand, though I could just be forgetting something.