For me that looks that Shepherd was brought to the main engine room. If he remained there or was taken on deck we do not know.
I agree that Shepherd could have been taken to the main engine room. But I am extremely doubtful if he could have been carried up to the deck. It would have involved too much effort from others and going through confined spaces and up ladders etc would have been unbearable for a man with a broken leg. So, IF he was taken to the main engine room, then he would unfortunately have been left there.
There were at last also two mentions that Chief Bell was also on deck at the final moments.
If Shepherd died inside the ship then I believe it was in the main engine room.
I have read that too and believe it. If Bell and his men realized that there was nothing more they could do, they would gain nothing and help no one if they remained below to drown like rats. So, even if they knew that all lifeboats were gone, they would have come up to the boat deck. And if Chief Engineer bell was seen on the deck, it means that he made sure that all the others (except Shepherd, IF he had been taken to the engine room) had also come up - Bell probably was the last to arrive.
Therefore, I still feel that poor Jonathan Shepherd had to be left somewhere deep inside the ship and it may well have been the main engine room. I think what you are trying to say is that if he was left there, he would probably have still been alive when the final plunge started because of the still dry engine room. IF
that is the case, then others would have died before him eg those who fell, those crushed by the falling first funnel etc. I suppose it is possible.