Taiwan - Shenzhen - Hong Kong Airport - Taiwan

Yes, itinerary Taiwan - Shenzhen - Hong Kong is definitely eligible for 144 hours visa free transit in entire Guangdong province. Here you have to take care about several following details:

- Between your scheduled arrival in Shenzhen and your scheduled departure by ferry from Shenzhen to Hong Kong airport there has to be at least 25 hours difference to be eligible for this scheme. If you intend to stay less than 24 hours you will not be able to use visa free transit because on 24 hours visa free transit it is not allowed to travel to Hong Kong or Macau from Shenzhen!
- You will have to book your ticket for ferry even before your departure from Taiwan. You can do it thorough CKS - Chu Kong Passenger Transport Company website. They operate ferries (in reality catamarans) from Shekou Shenzhen port to Hong Kong airport.
- You will HAVE TO use exactly that ferry that you have bough your ticket for.

Basically this is it.