LED beacons don't have the bright red cap of "normal" anti-collision lights.
On the 787, the top and bottom anti-collision lights (AKA rotating beacons) only look red when lit. When not flashing they are an unsuspecting dark spot.
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Photo from Reddit:
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I'm not home now, but looking at photos online seems like other brands have replicated this more accurately. Even in 1:200 scale, where jewels are the standard, it seems like at least GJ has opted for a discrete black dot on the 787. Can anyone with one handy confirm this?
Of course, we are delving into legit rivet-counter territory, and this opens up a can of worms. For instance, the same can be said about the green and red wing tip position lights (AKA navigation lights), which I think are one of the coolest features of precision scale airplane models dating back to the Herpa Wings 1:500 1st. gen. Many nav lights are also LED nowadays, and the cover is clear. Older airframes can also be retrofitted with LEDs, and you can find multiple light bulb variants on the same aircraft type.
I don't think it is a huge deal, but I do believe omitting the red jewel is safer in this case.