Here's the explanation:
The Atmos titles have 7.1 THD audio and use a complex seamless branching protection scheme. The audio dropout issues are the result of that combination and have nothing to do with the Atmos encoding. The BDP-83 is actually quite capable of bitstreaming Atmos audio in its 7.1 THD wrapper. Without getting too far into the technical reasons for this issue, suffice it to say that 7.1 THD requires more processing power to bitstream when combined with the complex seamless branching, and many older players don't have the poop to handle it. Think: buffering issues. DTS-MA 7.1 does not create these problems even with complex seamless branching.

If you have the capability to rip a BD and eliminate the seamless branching - burn that to a BD-R and the Oppo should handle it fine. The Oppo 93 has the same problem, the newer 103/103D do not since they have a dual-core chip and more memory.