In 5e, at least, proficiency bonus is based on character level - so your proficiency bonus goes up at level 5, regardless of whether that's five on one class, or one in five classes. In your example, they'd be level 9 (2 Bard/7 Cleric), have a proficiency bonus of +4, and so Jack of all trades would add 2 to all non-proficient ability checks.
I'm presuming, without being able to say with certainty, that BG3 gets this correct.