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From a roleplay perspective, I think you're totally right - it makes most sense for people to be weak to the sins they exhibit.
In-setting, I think the explanation is something along the lines of "Because these sins are fundamentally tied to forms of magic, it is that magic that is bolstering the character, not the sin itself." Another possible explanation might be "because Runeforge was built to accommodate certain behaviors, sins, and personalities, the location itself bolsters those who match its intended purpose."
Where I think this gets strange is runeforged weapons. People are bolstered by weapons that... are meant to destroy them? While I totally understand wanting people to wield weapons matching their sin/virtue, I prefer them to wield the weapons of a sin or virtue that OPPOSES what they're aiming to destroy. So, for instance, Domineering and Jealous weapons (those that include enchantment magic) should be the most powerful in the hands of the lustful or loving.
For flavor descriptions, I would suggest that certain wings of Runeforge "make you feel at home" when your sin matches those of that wing's creators. It is the natural belonging that empowers them, even when it comes to resisting sin - because it also empowers them to indulge their sin. If that is how they are naturally inclined, they likely don't need magical compulsion to act that way, after all.