I’m not certain but this is how I think it could work:
The special levy presumably has a due date, interest is payable on any amount that has not been paid by a lot owner after that date. This is the same for any amount of arrears such as being late with the ordinary levy.
If the Owners Corporation (OC) has taken out a loan, then the OC as a whole is liable to pay the interest on that loan.
I assume that when everyone pays the special levy, it will be enough to discharge the loan.
If the loan interest is less than or equal to the interest payable on arrears, then, in effect, the lot owners who have not yet paid the special levy will be covering the OC’s interest cost.
In the ACT legislation and probably elsewhere, there is also a provision to bill lot owners specifically for costs that are incurred by the OC due to some failure or negligence on the part of a lot owner. It might also be possible to use that sort of provision to cover any short-fall in the recovery of interest costs.