Hi, as you pointed yourself, other "players" do that (frontends), tvheadend is the backend.
what wonders me is that kodi on ATV cannot deinterlace, works here fine on android, windows and linux (im no apple user).
if TVH shell do the deinterlace only option would be to transcode afaik (its a option in the codec profiles), not stream profile.
so may try another player like mrmc or so (former kodi dev there who seems to be very good in things like deinterlace) or try at kodi forums
as there is the place to look for if deinterlacing doesnt work in your setup.
backend provides the original stream (interlaced)
frontend play the stream and deinterlace (best would be also hw acclerated)
hope this helps a bit ...