The only reason Mold Breaker is on that list is because of Magic Guard.
While Magic Guard is not listed on Bulbapedia's Mold Breaker page as one of the abilities Mold Breaker negates, there is an explanation:
>Mold Breaker does not affect Magic Guard as Mold Breaker only activates while the attack is in progress. This therefore means that Mold Breaker does negate Magic Guard, however, it is only during the split moment that it is negated. After the attack, Magic Guard returns, and then weather damage, poison damage kicks in.
This makes perfect sense as 1) Mold Breaker only negates the effects of abilities that protect against attacks, while 2) Magic Guard protects the Pokemon against indirect damage.
Source (Game FAQs)
In the case of your question, Flame Burst does not bypass Magic Guard, meaning Magic Guard is one of the few things that protects against Flame Burst's 1/16 damage, and this is still the case even with a Mold Breaker Pokemon on the field, which should cause a Pokemon with Magic Guard to take damage from Flame Burst side effect, but doesn't.
Smogon BW research thread