so you will never able to store ATMOS or X as PCM as output of each speaker will depend on their location relative to listener
That is what Dolby TrueHD is (on Atmos discs), an extra sound track stored as separate channels, for decoding on equipment that does not support Atmos decoding, like MC. So why would anyone try to decode Atmos and store it as PCM when a 6 or 8 channel soundtrack is already there? As you said, Atmos will be decoded and separated into channels, which in turn are sent to each speaker, specifically for your configuration. So a stored multichannel PCM track from Atmos will have very little value because it will only work on your specific system.
What we're looking for is an Atmos decoder, which now exists in Atmos compatible recievers and processors, for Windows. So that if I for example have a 12 channel system set up, the Atmos decoder will separate the track into each of the speakers based on the configuration I have set up and then send it to a multichannel DAC or sound card, which is what the receivers/processors to today when they get an Atmos signal.
And as with all previous hurdles, which at the time also were predicted "oh it is impossible, will never happen, will take many many years" etc. , like HDCP, 3D, Blu-ray menus among others, it is just a matter of time before a HTPC can decode Atmos just like any receiver on the market. Just wait and see. Usually it starts with a software company getting a licence to make a decoder into their software, like PowerDVD and Total Media Theatre have done in the past. (Remember when we had to copy a DLL from a TMT installation into some MC folder to make MC decode DTS-HD?)