Can Bellows Breathe target Ruin Runner in base?

No, you cannot target Ruin Runner with Bellows Breath, regardless of whether it is in the base or on a battlefield.

Ruin Runner has the ability: "I can't be chosen by enemy spells and abilities."

Because Bellows Breath is a spell that requires you to choose targets (as confirmed by Rule 352.14.a: "If a card specifies that an amount of damage may be split among some number of Units, then each Unit chosen is Targeted"), it is blocked by Ruin Runner's protection ability.