Not sure what the ACN is for the A380 but it does have two additional main gear boogies over the 777. It wouldn't surprise me if a fully laden 777-300ER had a higher ACN than a 747-400 or A380.
SQ A380 would also have had a low fuel load. 14.5 hours worth of fuel is a lot.
I do think there is probably more to the story than just PCN/ACN issues. However, I can certainly imagine that Angkasa Pura might have said the runway would be strengthened in time and weren't able to the meet the deadline.