makemkv has supported this for awhile now. The issue as you noted are the keys. You still have to pull the keys in order for it to work. Which requires a very expensive piece of software. Unless you know of another way to find these keys?
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itunes doesn't support MKV and you need MKV for HD audio and atmos. Otherwise you're stuck with MP4/M4V. Just use infuse and ditch itunes all together. You still lose atmos with the ATV but at least you can get the HD audio.H264 or h265? If h265 what extension? iTunes will stream 4K to AppleTV in the Computer section? Is there a new icon for 4K that can be set, like HD icon? Does handbrake correctly do Enhanced Dolby Digital 7.1....and can it interpret the newer object orientated sound streams (Atmos) that are on 4K discs?
I’m not attacking, there just isn’t good info out there yet.