Have you tried asking Samsung Support? Regardless of where the cause is, they may be aware of this issue and may know of a way to work around that. It could be as small as a non-obvious setting.
Have you tried asking on a Samsung soundbar user forum? Other users may have experienced the same or similar, and may have their own unique perspective on this issue. Some smart user may even know a solution.
As this audio system is one of Samsung’s higher tier home cinema items, I would have expected a more flawless usage.
Apple TV outputs Dolby Atmos in a Dolby MAT stream, which is different from Dolby Atmos packed within a Dolby Digital Plus stream, as other equipment (like a smart TV) might use. Maybe that plays a role. As audio comes in later, that means that Dolby MAT is supported (understood), but maybe the change in format causes a delay?
I don’t experience this issue through my AV receiver. If some reader here has the same audio system as you have, I ask them to give their input on this. Thanks.