I think a big reason why c!drunz isn't the most healthy couple is because they aren't two people who mutually chose to be together.
C!drunz is two people who don't have many other options. They're two people that have been forced into their roles, self-induced or otherwise, and therefore forced together. C!Dream needed someone he could trust. C!Punz believed in the cause, and any doubts were easily dismissed by a little gold and jewels. It's a boss who only has one employee and an employee who sees other potential bosses as completely incompetent.
Their love is as real as it can be for their situation. It's as real as any love that forms during the final days of mankind. Love born from the apocalypse.
When you spend enough time with someone, knowing there's no one else, you grow to need and resent that person. A part of you wishes you met on different terms, but you also know if you did, you wouldn't love them like you do now.
C!drunz didn't choose each other, not willingly. They didn't have a chance to learn and grow and reconcile their differences. The reality is they've settled, and they come to terms with that in different ways.
C!Punz wholeheartedly accepted it. Perhaps they never experienced a connection so deep, so engrained in his being he doesn't know where they end and c!Dream begins. C!Dream is... not thrilled. He knew what it was like to have friends, people he called his soulmates. Whatever he and c!Punz have is not that.
He still cares about c!Punz, a lot. He loves them, truly. As truly as love can be when they both have a foot in the grave.