The only cases I am aware of where pcm causes an issue is with certain soundbars, and/or when using ARC out of a TV. Otherwise the audio is identical to bitstream and receivers can still handle the surround sound and everything that goes with it. And as you mentioned lossless Atmos is the limitation of this. Nvidia shield seems to be the alternative of choice for playing bitstream and 4K Dolby vision from UHD Blu-rays.
I have been using infuse for 5 years now and been working great and i use it for everything except 4K content because of the previously mentioned limitations.
This thread has some info about an HDR issue but from what I gather it only affects some people/TVs.