What is this creature/machine?
The birthing of Kryptonians, as we know, is no longer "natural" but is an automated process.
Clearly the creature/machine is just part of the handling process of the gestation of new children.
The Genesis Chamber was fashioned on the planet Krypton to house the Growth Codex and all unborn Kryptonian gene seeds that would occupy prospective Kryptonian generations. Aquabots were utilized to control and preserve the Genesis Chamber so that no Kryptonian would ever enter or interfere with the birthing procedure.
Why is it removing the baby from the tree pod?
Well, we don't know precisely but, from the image, it seems that the baby is full term and ready to be "born".
Essentially, it seems likely that that this baby is "ripe" and is being removed from the Genesis process to be handed to it's new parents.