I worked on a project with puppeteers in green using puppets against a green screen. I was actually hired to help clean it up because even though it was lit about as well as could be, shadows created under the puppeteers arms etc, made a ton of artifacts. This was a long time ago, and keyers have gotten better since then, but I’d still expect a lot of roto cleanup.
Another thing to keep in mind, not only were there keying artifacts, there were many places where a puppeteer’s green stick or arm crossed in front of a puppet and erased some of the puppet. The erased portions of the puppet needed to be very carefully clone painted back in. Given what you are doing, I would recommend shooting the green man against a green screen. If the man is potentially moving in front of other actors, or moving objects in front of actors as you describe, you will want him as isolated. That should help keep any clone painting to a minimum. You could maybe compromise and set up a portable green screen on set behind the place that he will be interacting with things.
-Matt
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