In the Shruti sources we find many statements that Lord Prajapati is Supreme Self. For example Shatapatha Brahmana of YajurVeda in 184.108.40.206 states
Verily, Prajâpati alone was here in the beginning. He desired, 'May I exist, may I reproduce myself!' He toiled, he practised austerity (or, became heated). From him, worn out and heated, the waters were created: from that heated Person the waters are born.
So, it means Lord Brahma alone was in the beginning and he existed as per his desire. This shows he is a Supreme Self. There are also other plenty of verses in Vedas which show that Lord Brahma is Supreme Lord.
But the same Shatapatha Brahamana also states:
Pragâpati conceived a passion for his own daughter... 'May I pair with her!' thus (thinking) he united with her. This, assuredly, was a sin in the eyes of the gods. 'He who acts thus towards his own daughter, our sister, [commits a sin],' they thought. The gods then said to this god who rules over the pashus (Rudra), 'This one, surely, commits a sin who acts thus towards his own daughter, our sister. Pierce him!' Rudra, taking aim, pierced him.
Now, the above passages hints that Prajapati is just a transmigrating Jiva as it shows he is attached to Karmas. There are also other instances like his birth is stated:
He who is the first among the Gods, that Rudra who is the great seer who is higher than the Universe, he is the one who saw Hiranyagarbha being born. (Taittariya Aranyaka 11.12)
So, Vedas at some place say that Prajapati is Supreme Self, all is his form, he is Atman of all etc.. etc... At some places Vedas also say that he is attached to Karmas, seen being born (ie. Having birth etc.. ) which is character of Jiva. So there is contradiction itself in the Vedas.
Do any scripture solve this exact issue raising the points from both sides of Shruti? Have any philosopher / commentator solved the above contradiction about whether Prajapati should be seen as Supreme Self or Transmigrating Jiva by raising the points from Vedas?