You could actually have the 2.8.9 configuration, putting the last electron in a 3d rather than 4s orbital. But the 2.8.8.1 one is lower in energy and thus more stable. How electrons fill subshells in neutral atoms to make the lowest energy configuration can be seen here.

It sounds likely that you are taking your image in very low light, where the shutter speed is slow enough in either case that the camera's auto-exposure program is choosing the higher ISO in either case. There are probably some situations where it might leave the shutter alone and lower ISO first. It depends on the situation, your camera, and the settings you've chosen.

If you want the camera to do something outside of its program, you will need to take it out of auto mode, where, yes, you'll find that your faster lens lets you use about half the ISO at the same shutter speed. That's not a huge advantage — really, when you get to f/2.8 and faster, you kind of get diminishing returns for increasingly steep costs. If you are going to be using a tripod and don't care about exposure time, you're absolutely right that it isn't crucial to spend more for faster aperture alone.

If you care about taking photos hand-held in low light, though, it really may be worth it, and the camera is probably doing the right thing for you. It's impossible to hold completely still, and having the shutter speed can make a big difference.

But the faster lens may have some other advantages — it may have nicer rendering independent of exposure, be sharper stopped down, or have other features.