A “simple” transistor or relay is bulky and expensive. By comparison, routing through a programmable chip (which is already on the board) is nothing more than routing work—it doesn’t add anything to the BOM.

This is just the way people design circuits these days, because it’s easier and cheaper. A single µC with a few GPIOs, rather than a bunch of logic chips scattered around the board.

Even on programmable chips, not every part of the chip is programmable.

The goal is to make this so it cannot be overridden in software. By designing hard-coded logic in a chip that already exists, you can get the same level of security for essentially zero cost.

Especially, even if this is programmable, this chip is probably not programmable from the point of view of the motherboard...

And if an attacker is able to connect a chip programmer on your motherboard, you have a totally different threat model and bigger problems to worry about.

because it already has to go through it for signals processing

Why should it go through yet another redundant mechanism.

Have you ever seen a MacBook from the last 10 years? There are no physical switches, it's an hall sensor that works with the magnets that keep the thing closed.