Well, I had hoped to find something in the layout of the formation, but I can't find any significant matches so I'll just post my thinking in case someone else has better insight.
-----
We've established that the spikes can be higher or lower compared to the center, depending on the slope of the terrain, which indicates that the formation is made up of separate independently positioned objects, rather than being a single 3D model for the entire formation. That struck me as notable, since it seems to me that it would be simpler for the entire formation to be one model which could be spawned and rendered at a single position. Instead, Frontier clearly asked their artists to create the individual pieces of the formation separately, so that they could be positioned independently of eachother. Why would they do that?
Since the barnacles are clearly meant to be at least semi organic, and E

already uses procedural generation to easily create variety in other contexts, one easy explanation would be randomness. Individual 3D models would allow the spikes to be randomly positioned around the central barnacle, which would give the formations an even more organic and varied appearance (as might be expected from something growing up through the ground). But we've ruled that out: every formation, even in different star systems, has exactly the same layout. That means instead of whipping up a quick randomizer, someone at Frontier had to manually position every spike in the formation, record all of those positions, and program them in so that every time a barnacle formation spawns, it gets exactly the same spikes in exactly the same relative positions. So again, why would they do that?
Another possible explanation is, of course, that the arrangement has some meaning. In this scenario, it seemed plausible to me that the designers might have asked the art department to work on the 3D models in advance (since that pipeline can be somewhat long), leaving them free to decide later on exactly what the layout was going to be in order to encode the intended meaning.
So I started looking at the layout:
View attachment 98649View attachment 98650View attachment 98651
The first thing I that struck me was that many of the spikes seem to form slight arcs, spiraling out from the center (and indeed, the central barnacle itself has a distinctly spiral kind of appearance). That made me think that perhaps it was meant to be indicative of the spiral arms of the galaxy, and combined with the fact that there are always exactly two fruit-bearing spikes, I thought maybe the entire formation was meant to be a kind of map: if we could use the overall formation to align it to the galaxy map such that one of the fruits matched a known reference point (such as Sol, or the Pleiades), then the other fruit would point to another area of the galaxy. I had hoped that when zooming in on that area, we'd find a nebula that was an even more exact match for the symbol on the central barnacle.
But I haven't had any luck with that. The two fruit-bearing spikes (in yellow above) are too close to the center for either of them to correspond to us (since we're relatively far from the core). My next idea was to look for especially large nebulae, or pulsars, or something else that might line up with this arrangement on the galactic scale, but I couldn't find any clear matches there either.
So that's where I've left it for now. Hopefully someone else will see a pattern here, if there is one.