Does the limitation of the prepaid amount being multiples of $1,000 apply when making online payment?

Yes, it does.  According to Setting Unit(所校郵資單位) in the schedule to the licence, the credit amount must be multiples of HK$1,000 for all digital postal franking machines and this limitation also applies to value crediting made by online payment.  The Postmaster General reserves the right to terminate the licence should there be any breach of the licence terms and conditions.