His relationship with Penny started selfishly--like he was trying to atone for past mistakes: abandoning his own sister, time lost to addiction, and all of the people he'd let down. He saw his past self in her blown out pupils and thought maybe he'd get it right this time.
But he learned quickly that Penny was her own person, not someone who needed to be saved. She was so brave and quick to smile. She just needed someone to believe in her and hold her hand.
He found himself driving up to coast to visit her in rehab and when she was home, he made every excuse to check on her. Oh, he accidentally ordered too much food. He needed someone to keep him awake while he finished a painting.
Eventually he gave up on the excuses. That's how he found himself wearing a face mask eating takeout Chinese food on the floor of his studio. He bought a futon because he couldn't let Penny sleep on the floor. She had a spare tooth brush in the bathroom next to Fitz's, Jesse's, and Elby's. He could grumble all he wanted, but no one would believe that he didn't want these people taking up space in his life.
If anyone asked if he cared for Penny, he'd say "don't ask stupid questions." But if you caught him looking at her, he'd be smiling at her like family because she was.