I am very sorry that your experience with the Putri Papua was so negative. My wife and I have done 25 dive trips with to Indonesia with Grand Komodo since 2001, many of them in that boat. We do not have any affiliation/funding with their company, simply we have been returning to them because the excellent service they have provided consistently for us and our guests. We have written many positive reviews in Undercurrent and other blogs over the years.
Their boats are small, we like that because we prefer small groups, sometimes we have been the only passengers. The cabins are small but clean and we have found them confortable. The Phinisi hull design is old but not antiquated, a majority of liveaborads in Indonesia share it. The company regularly fumigate their boats and take precautions to avoid rodents or other pests from climbing aboard when in the harbor. Frankly, we live in a semitropical area and know well how difficult it sometimes is to keep pests at bay and they do a good job.
The Putri has rubber mats glued to the deck in diving areas, but fall are always possible in such a wet environment. I have had some falls myself but mostly due to inattention on my part or sudden sea surges. They always encourage all the guest to report any accidents on board to the cruise director to evaluate the care needed. Being a physician I have been happy to help some times when needed.
We have always found that the engine has been powerful enough to deal with the currents of that part of Indonesia, it appears to be well maintained as well as the compressors and all other boat equipment. Nobody has had "bad air" during any of our trips
The only time that we have heard a guest complaining of engine exhaust smell was from my brother in law 13 years ago on a particularly difficult crossing to Wakatobi.The crew was able to minimize. Possibly they might have helped if you told them.
Regarding your friend's experience, we have done the trip Alor-Banda-Raja Ampat several times in both directions and know how rough the crossing to Gunung Api and Banda can get. Since we are going on the Putri again in a few moths, I contacted the owners who explained what happened to my satisfaction. Portholes or pump failures may happen in any boat during extremely bad weather (that prevented other liveaboards from sailing) but the captain and crew dealt with the situatione fficiently and brought their divers safely to port. My understanding is that when they rejected alternative places to dive, they were refunded their money, which is not common in the liveaboard industry.
Again we are sorry you had a bad trip with GK but felt that other members were entitled to read about our different experience with the company and the boat.