You are right. Currently, fighting with two weapons doesn't work as intended (at least not according to default 5E rules). Main hand is correct, you get proficiency and attribute modifiers on the attack roll and attribute modifier on the damage roll.
What the bonus off-hand attack should have:
- Proficiency and Attribute modifiers on the attack roll
- Neither on the damage roll
What the bonus off-hand attack actually has in BG3:
- Proficiency bonus on the attack roll
- Attribute modifier on the damage roll
This seems like a simple bug that should be fixed in a future patch.