According to this account of the sinking of the Kachidoki Maru, a British PoW encountered a young woman he deemed to be Japanese with an infant on the bamboo raft he boarded after the ship was torpedoed.
Later on, he reports that two Japanese seamen, who already had a raft of their own, attempted to board his raft with knives drawn, and he says they aimed to get to the woman mentioned. He does not specify what he thought these seamen intended to do when they got to her, but he does wonder why the woman was not placed on a lifeboat in the first place, and says that he and his fellow PoWs attempted to keep the sailors off of their raft.
Here are the relevant quotes, extracted from the original I linked to above -
The woman is first mentioned:
Another hour passed, the sun began to appear and for miles around we could see survivors clinging to rafts and suchlike, also lifeboats laden with Japanese. On our raft, which was made of bamboo and about 12 ft square, there, seated at the centre, was a young Japanese woman clutching a baby. Why that young woman was not put into a lifeboat was a question that only the Japs could answer. Maybe it was one of their stupid customs.
And the episode with the Japanese seamen:
Later in the afternoon we saw smoke again in the distance and this turned out to be a couple of Japanese frigates. They lost no time in picking up the Japs in the lifeboats. Whilst this was going on, two Jap seamen, who were on a raft similar to ours, were trying to paddle their raft nearer to us and each had a knife in their hand, their intention being to get to the girl on our raft but we had other ideas. Each time they got close, we would push them away with our feet and this infuriated them so much that when they did eventually get aboard they started to strike out at everyone.
I do not know how many got knifed because, being on the edge, I slid off the raft and swam towards an empty lifeboat vacated by the Japs.
Apart from these two passages, the woman is not mentioned again, leaving me with these questions:
So consulting a Japanese text on the sinking of the Kachidoki Maru gives the answer to your first question.
翌朝10時頃、救難船が沈没現場に到着、兵士、次に婦女子が救助され、捕虜の救助はその後になった。
The order of lifeboat priority for the crew about the Kachidoki Maru was soldiers first, women and children second, POWs last. This might seem strange to those familiar with the western "women and children first" policy, but we have to remember this is a relatively recent cultural phenomenon dating to 19th century America, with no basis in maritime law and no relevance to Imperial Japan. So this woman was presumably one of many not prioritised over Japanese soldiers.
What might a woman with an infant have been doing on such a ship in the first place?
Many possibilities exist. Perhaps she was a member of the kaitakudan (settlers) sent to live in newly annexed territories of the Japanese Empire and expand its influence as nurses, teachers, clerks, cooks, and wives of Kaitakudan soldiers - in Singapore, teachers would have been especially in demand with the establishment of new schools to teach the Japanese language and culture. Especially in Manchuria, many such women were left behind after the war ended, and found new lives marrying Chinese men; perhaps she was on her way back to Japan, in fear of this.
Could our PoW narrator have mistaken a "comfort woman" from elsewhere in Asia for a Japanese woman (i.e. were any such women kept aboard Japanese Navy ships)?
Remembering that this is specifically a transport ship, the answer is yes, comfort women would have been transported on such ships. In general, however, it would be rare to send them in the opposite direction, from the colonies to Japan, as they would primarily work in service of military bases set up in the various colonies. Especially given the presence of an infant, it seems far more likely she would be Japanese and returning to her homeland.