Beware of Potential Spoilers below for Annihilation
You seem to take it that the Annihilation
needs the gag in question or else the audience not only won't "get it," and that this as a formal necessity which is required to sustain the vehicle via the tenor. But is this message really there? And if it is, is this something that audience needed to get? And did the gag in question signal the message that you think it signals?
As for the first question, it seems to me that the film is about destruction and decay as a magnet. That is, it's not simply random trauma, but self-destruction as a design feature. It's something built into us as a drive, biologically and psychologically, a drive that terrifies us as much as it attracts us.*
As for the second question, if we cannot definitively answer the first question affirmatively, then this question already falls. Supposing that your reading is correct in the sense that this is a preferred ("right" or "more right") reading, then we need to ask if the audience needs closure on the question. It is true that if you want your audience clearly to arrive at a particular conclusion, then you have to provide them with hints, clues, cues, and possibly even direct exposition. Not all artworks, of course, are "closed" by the evidence. What's more, artworks are not necessarily damaged by lack of closure. Think of, for example, the lack of closure regarding glimmering eyes in Blade Runner.
Why do we need closure on this particular point? And we should also consider that the price of "surety of closure" is that we might rip the delicate fabric of the dream by overemphasizing the point. No one likes to be beat over the head with "the message." Turning again to Blade Runner
, think of the exposition where Deckard over-explains the meaning and significance of Batty's sacrifice. Think of Deckard's leaden narration that weighs down the rest of the film. Is it worth it to get your point across at the expense of puncturing aesthetic purity (and even reality) of your tale?
This is a lesson I think that today's SJW scriptwriters need to take into greater consideration, as they so often beat the viewer over the head with the message (Sabrina on Netflix is rife with this painfully overt coding).
Finally, I am not sure the drum riff gag at the end of the film signals what you think it signals. It is very common conventional feature of horror and science-fiction tales to have a THE END - OR IS IT? gag at the end which simply signals that the danger is not past. Even if the intended message is to preserve a balance between vehicle and tenor and to sustain the tenor via the vehicle, the formal/conventional cue here (which is driven by genre expectations) is that of a simple gag. Thus, even if we feel the need to have the audience clearly hear the fall of the tree in the forest, they may not be perceiving the sound we want them to hear, thus denying us closure.
*In a larger sense, self-destruction and decay is which is a feature of all lifeforms and the universe itself as entropy. The whole universe is tilting toward decay. Outside of Brownian motion, patterns of life are the most notable exception to the rule of universal decay. Life organizes and increases complexity in its arrangement of matter. Life's great trick is to turn decay in on itself for advantage. Mutation, an "error" in the perfection of a signal, when combined with reproduction can accidentally/contingently transfer fitter genes to off-spring via natural selection. The genetic shuffling of sexual reproduction is the same trick. However, the introduction of the next generation implies the need for the older generation to get out of the way--thus death and decay in the individual organism is a necessary feature for life to temporarily win its contest to stave off death and disorganization.