Is Sri Kurma an avatar of Prajapati?
Yes, it's already described in your question itself and in the answer which you have linked.
The word praja means subject and the word pati means master. It's a post or title. There are many Prajapatis identified in scriptures, Lord Bhrahma and Daksha are most famous. Additionally, Padma Purana mention
Lord Mahadeva replied-- Lord Brahma had created numerous Prajapatis like Bhrigu, Marichi, Atri, Daksha, Kardam, Pulastya, Pulaha, Angira and Kratu.
So, now let's assume that Prajapati mentioned in the Shatapatha Brahmana (184.108.40.206-10) is Lord Bhrahma. So,
Lord Brahma indeed is the Kurma avatara?
Note: This doesn't mean that Kurma is not Lord Vishnu's incarnation. Please see below explanation.
If both stories contradict then as per the tradition shouldn’t we accept the Vedic reference?
Yes but only if both the stories are from the same incident which happened in the same Kalpa/Manvantara/Mahayuga/Yuga.
Let's see few more confusions:
A. Who is Daksha?
Answer 1: Daksha is Lord Bhrahma's son who became Prajapati.
Answer 2: In Dhruva's line there was a king named Prachinavarhi. Prachinavarhi had ten sons, known as the Prachetas. Daksha was son of Prachetas and became Prajapati.
Now both the answers are true as both are from different timelines.
The sages interrupted Romaharshana. They said, "Sage, we are completely confused. We have heard that Daksha was born from Lord Brahma's toe. And yet you have told us that Daksha was the son of the Prachetas. How is this possible?"
Romaharshana replied, "There is no reason for confusion. Many Dakshas have been born to rule over the world. One was born from Brahma's toe, yet another was the son of the Prachetas." - Creation chapter of Bhrahma Purana.
B. What is the story of Godess Lakshmi's birth?
Answer 1: Godess Lakshmi emerged during Samudra Manthana and got married to Lord Vishnu.
Answer 2: Godess Lakshmi was daughter of Bhrigu and Khyati who later got married to Lord Vishnu.
Here too both answers are true.
Godess Lakshmi was actually daughter of Bhrigu and Khyati. Indra showed disrespect to her (or sage Durvasa in some stories), she made her abode in the abysmal depth of the sea and later emerged during Samudra Manthan.
MAITREYA.--It is commonly said that the goddess Lakshmi was born from the sea of milk, when it was churned for ambrosia (i.e. during Samudra Manthana); how then can you say that she was the daughter of Bhrigu and Khyáti.
PARÁŚARA.-- read the reply from Vishnu Purana.
C. Who brought river Ganga on Earth?
Answers may be Goutama, Vashishta and Bhagiratha. This is explained here.
D. Lord Ganesha's birth story?
Read the two different stories from Shiva Purana and Varaha Purana. Here too both the stories are true as both are from different timelines.
Similarly, it's heard that Dhruva is a great devotee of Lord Vishnu but one story mention him as a devotee of Lord Bhrahma. Is Dhruva portrayed as a devotee of Prajapati Brahma in any texts?
Here too both stories are true as both are from different timelines.
Conclusion: Kurma in one Kalpa/Manvantara may be Prajapati's incarnation and in some other Kalpa/Manvantara Lord Vishnu's incarnation. There is no reason to doubt on the fact that Kurma is Lord Vishnu's incarnation (during Samudra Manthana - in 6th Manvantara). At the same time, Kurma being Prajapati's incarnation (in the beginning of creation - in 1st Manvantara) is also TRUE.