You are correct that the chip does, of course, interact with light because of the transparency. In typical applications, the housing would be opaque, and the chip kept in the dark. If you open an iPhone, for example, many of the chips have the exact same construction as this, and they are similarly photosensitive, but they are inside the iPhone case so it's not a problem.

However, for example, if you shine a laser pointer at the back side of the chip, you'll cause it to glitch. This is true both for the Baochip, and for the chips inside the iPhone. In the case of the Baochip, generally, this will trigger an attack sensor and the chip will reboot or go into fail-safe state, but a very precise laser pulse can escape detection, and thus form the basis of a glitching attack.

The Defcon badges were deliberately constructed with transparent plastic to highlight the inspectability of the chips, but if you have an actual concern about people attacking the chip with lasers or you plan to operate this in some environment constantly filled with bright strobe lights, the recommendation is to put some dark epoxy over the chip after you're done inspecting it.

The idea is that it's easier to put the epoxy on after inspection, than it is to remove the epoxy, inspect it, and then put the epoxy back again. This trades off against the assumption that supply chain attacks are a more scalable attack vector than direct physical attacks.