What are the Trek Domane frame bottom hex screws for?

The braze-ons beneath the down tube are traditionally for mounting a third bottle cage. Of course that bottle is more exposed to road dirt than the others, so many people use it for various utility purposes. (You can get water-bottle-shaped repair kits that will fit in there, batteries, air reservoirs for air horns and I'm sure other things as well.) It would definitely be a reasonable place to mount a small pump.

Braze-ons on the top tube are relatively new, but there are a number of small bags available that bolt on there. The advantage of these bags over normal (velcro-attached) top tube bags is that they are better affixed, so they're not going to start to tip over on you as you're pulling out a bar. You can also get computer mounts for some brands of bike computer/navigation systems.

Cable management might be an issue, but a bottle-shaped battery pack with USB out could be very useful for long rides or an older computer whose battery no longer has good endurance.