I mean, it certainly would be a huge tradeoff for them, in terms of development resources. They would have to completely reengineer the entire way the Apple TV handles audio at its core, and provide a switch to switch between the normal way and this new method. They would also have to figure out some way to "grey out" in the interface all the features that would be disabled... not to mention that even something as basic as user interface sounds wouldn't even work. It's just very un-apple like to compromise the quality of the product that badly. Then, going forward, their development load would essentially be doubled, as they would be having to maintain two completely different systems simultaneously.
I'm not saying they couldn't do it, but I'm saying that it would not be a useful allocation of resources. Especially because this same problem could be fixed so much easier by just adding support for decoding TrueHD with Dolby MAT, so that TrueHD atmos content could be sent over LPCM with atmos intact, just as DD+ atmos already is. The lack of passthrough is not really even the issue. But my guess is that they would have to pay Dolby an additional licensing fee to add that functionality, and since the only benefit of doing so would be to improve an "off label" (so to speak) use of the AppleTV, one that some might even argue is somewhat murky in its legality, I can see why it's not a high priority for them. But I still wish they would also.