You will lose a day in travel getting from Boracay to Bali due to the plane changes you will have to make in Manila and the time you will have to allow for your transit.

If it was me, I would choose either Boracay or Bali, but not both.

Fly directly into Hong Kong, spend 4/5 nights, then fly to Boracay via Manila.
Even if you catch the 9am flight from HKG to MNL, (you will have to wake up 6am) you will land in MNL at 11am, transfer to the other terminal and get a 1pm flight, landing at 2pm in Caticlan, transfer via tricycle to the ferry, then transfer to another tricycle, getting to your hotel at around 3pm.
My point being, 3 days in Boracay is only just enough to justify the travel to get there and back.

Alternatively, DPS is a direct flight from HKG on Cathay Pacific (also Garuda now flies daily I believe).

To go from MNL to DPS, you are going to have to make one stop (try Garuda, Philippine Airlines or Cathay Pacific), but remember you will have to consider the time it will take to get from Boracay to MNL, allowing for delays and terminal transfer. So a whole day would be lost in travel.