Here is what I gather from both trip itineraries:
Triton Bay-Sorong (D2) covers a lot more distance (as shown in black line, above) with more of open sea from Kaimana to Misool than Sorong-Misool-Sorong (BM, as shown by the red line, above). Therefore you would spend more time on sailing than diving on D2 than on BM, as indicated by the numbers of dives 30 dives in 10 days for BM vs. 35 dives in 12 days for D2.
Misool-Sorong itinerary of both trips would be the same. However you will do more diving in the Misool area with BM with less sailing time than with D2.
The good thing about D2, it starts from Triton Bay. From watching the YouTube video, below, you may pass Bagan, where you can dive with Whalesharks like in Cendrawasih Bay or Sangalaki/Kakaban/Maratua. That’s an interesting experience. I’ve been to Cendrawasih Bay for similar diving. Basically you have 2 more days of sailing, diving plus a chance to dive with whalesharks for the difference in the price you pay.
Your flight time & cost will be about the same, flying half around the world, spending 30+ hours on flights one way to Sorong or Kaimana. I would pick the Triton Bay.
My concern is sailing in the open sea from Kaimana to Misool with Phinisi boat. I have done it in Cendrawasih Bay with Pearl of Papua. It wasn't fun during the storm. Another one was from Ambon to Banda Neira with La Galigo. We didn't make it & detoured to Ceram. After those experiences, I stick with big metal boat like BM for sailing on such passages.
Unfortunately I have never been to Triton Bay, but it’s in my bucket list. Hoping BM would do Triton Bay to Sorong some day.
Have fun diving in March 2020!