What was the reasoning for the lower vent mounted as such? Did you ask the builder?

The second one doesn't look like a dryer vent to me. Are you sure the other vent near there isn't the downstairs dryer vent and you have another vent upstairs somewhere. Either out of the roof or the siding somewhere else?

OK, so the builder got back with me. The upstairs dryer vents to the roof. He thinks the small pipe is the cold air return venting to the water heater.

"He thinks the small pipe is the cold air return venting to the water heater."

Shouldn't he know for sure? It is his project, correct?

The second pipe does not look like a dryer vent. It could even be part of the plumbing or exhaust (although those usually vent out the roof).

Just get yourself a small piece of galvanized hardware cloth with 1/2” mesh openings and bend it to form a plug that you can force into the pipe. An easy way to neatly form it is to get a short piece of the next size smaller pipe, clamp it, and use it as a form to hammer the hardware cloth into a tubular plug shape.

Looks like a water heater power went pipe, in any case, whatever it is, and as long as it's not a dryer vent it should have a screen.