If the personality of ShivBaba is seen in the Subtle Regions it does not mean that he has left the body. The body of light of Brahma Baba used to be seen in the Subtle Region even when he used to be in corporeal. In one Murli it is said that he /the Purifier/ has to purify even the Brahma of the Subtle Region. It means the soul of Prajapita can be in the corporeal world, but in the Subtle Region there can be his perfect form of ShivBaba.
This body of light there of course belongs to the corporeal personality of the Father Prajapita as Shiva the point of light does not possess neither subtle nor gross body and as you have pointed in the Murli it is said that he does not enter a subtle body.
However it does not mean that the task of ShivBaba is performed by this soul of the Father whose body we see there, like we have the body of Brahma Baba /and his light body even in advance/, but the role in his body is played by the Supreme Father, the soul of Shiva. This soul plays both a role of the mother through Brahma Baba and the Father through Prajapita /ShivBaba.