This kind of situation is up to the GM.
Pathfinder isn't designed to handle these sort of situations. The bulk of Pathfinder game mechanics are about combat and adventuring, not genetics. And no, reproduction does not fall under the crafting rules. The system simply doesn't have the rules to address it.
That said, some sections of the RAW for polymorph magic could be relevant here. According to the polymorph rules, a polymorphed creature does not actually change type.
Polymorph: a polymorph spell transforms your physical body to take on the shape of another creature. While these spells make you appear to be the creature, granting you a +10 bonus on Disguise skill checks, they do not grant you all of the abilities and powers of the creature.
For example, if a male human uses Alter Self to assume the form of an elf, his creature type is still "humanoid (human)" and not "humanoid (elf)". This might imply that the father still counts as "humanoid (human)" for the purposes of genetics. On the other hand, maybe as part of assuming the form of another creature, he also assumes their DNA and reproductive cells.
On the other other hand, polymorphing is magic, and magic often ignores conventional science and physics and biology and biochemistry. The polymorph rules don't specify all the consequences of taking the form of another humanoid race, but the RAW has a clause saying that these ambiguous questions are the GM's call.
While most of these should be obvious, the GM is the final arbiter of what abilities depend on form and are lost when a new form is assumed.