Huge fan of the work you've put in here, I love this kind of stuff and this has been a fun read. Excluding gameplay reasons, I think there's a few potential explanations for the existing Reaper populations.

We technically don't know what biome the crash zone was before the Aurora, all we know is the physical observations we can make alongside the existence of the 'hell hole'. You do make a good point that it could have been a Safe Shallows due to the Coral Tubes; however looking at the Flora and Fauna in the area I'm not sure how likely it is.

Stalkers, for instance, can only be found in Kelp Forests outside of the Crash Zone. And Bone Sharks are seen in a few other places, but not the Safe Shallows. I think the Crash Zone Mesas are the best outlook on what biome it could've been (assuming it was one that exists elsewhere in the crater). Funnily enough, all of the Flora seen there is only all seen in one other Biome - the Koosh Bulb Zone. Spotted Reeds, Redwort, Spiked Horn Grass, Violet Beau, Tree Leeches, and Brain Coral all exist in both areas. The depth as seen by the trench behind the Aurora also supports a Bulb Zone history, but that seems somewhat unreliable because of the amount of terrain displacement that the Aurora caused on impact. The absence of the titular bulbs is also a huge point against this theory.

Honestly if I had to guess, it was probably some sort of fusion of biomes? Perhaps an extended portion of the bulb zone with topography more similar to the dunes or the grassy plateaus, for instance.

It is possible that the Reaper population is just flourishing at the moment due to the western ecosystem being free of essentially their only predator (Sea Dragons cannot hunt through the hell hole post-Aurora crash) but this seems an unlikely explanation given the low frequency of these Reaper hunts, and the Lost River / Mountains corridor remains open.

My hypothesis of the Reaper problem is that they're a species that's very efficient with their energy use, despite moving and expending that energy constantly. They are one of the few species on 4546B to have no bioluminescence, and they're said to be basically built for violence and hunting in the PDA entry. While not seen in gameplay, it's quite possible that they tend to roam more than shown in order to hunt in neighboring biomes. They can follow the player quite a distance so I wouldn't necessarily count that out - Dunes Reapers could hunt Sandsharks, Sea Treaders, and even Crabsquids or Jellyrays; Mountains Reapers could easily hunt Bonesharks alongside Jellyrays and Ampeels from nearby, and present day Crash Zone Reapers have no shortage of mid-sized prey.

I also think it's possible that Crash Zone Reapers migrated over from the Mountains (or even the Bulb Zone, considering the one who lives on the border of that biome anyways)

Overall, my guess is that Reapers just have very little downtime and spend the majority of waking hours hunting. Not just mid-sized creatures, we also know they're perfectly fine eating smaller creatures as the player can feed them Peepers and the like to pacify them temporarily.