So here's the interesting thing regarding this: It's a loading zone glitch, and that isn't exactly an easy thing to fix.
Now, of course the fastest ways to fix this would be to make the chest a one time grab per instance, trigger a despawn of the asset and interact on open, or simply to cut the time at the end way the heck down.
But here's the thing, trying to prevent this without one of those things is almost futile in all honesty. Loading zones are built into the maps themselves typically nowadays, and can't just be "moved" without literally shifting the entire map around where it lay, or reworking the entire map on which the loading zone falls. For something like the Menagerie (which likely has the rest of the raid hidden nearby due to reuse of assets) this would be nearly impossible. Think about the Riven cheese. It hasn't been fixed for this same reason. That entire area is one giant map, and trying to just move that one loading zone or move the map to conform could cause an insane amount of glitches and possibly just an inability to use the asset. Now, of course in LW it's a whole different issue, but their best bet is to do one of the things I said above. Far easier to edit the interaction code, timer, or write code to trigger a despawn rather than fix the entire map.
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That is true, though I suppose they do that to play into that long timer (probably to let people explore a bit or who knows what) but they'd probably also have to lower it to 30 seconds as well to accommodate for this.