You can frequently avoid this by running at a lower voltage - SPI chips are often rated to run down to under 3V, and associated components will tend not to run with that much power

I tried to use something like this to read a flash on a car’s ECU. I even build a small probe station when the clip finally broke. I ended up having to desolder it. I don’t understand how hackers make in-circuit spi probing work on embedded systems. It always just magically works for them to clip a Pomona on and go. I don’t get it.

On PC mobos it's usually not a problem as the BIOS is programmed after assembly. I've seen laptop repair shops in China do it all the time.

Also you could potentially damage the on-board voltage converter/regulator, since most aren’t designed to be back-driven from their outputs.

Yeah, it's best if you can also hold down any reset lines on other things on the board.