Weird. I tried your model too and it works for me as well (the partial chamfer).
Then I took my first model, deleted the interior surfaces and recreated them using the Shell command, and then I could chamfer it in the way I first wanted to as well.
Do you know what the difference is between those two? My original model, and one recreated with Shell? Visually they look pretty much like the same thing.
In my original model, I created a sphere, used Shell on it, then boolean subtracted I think three other spheres.
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