We should go by the the Ramayana. If it says Janaka is the father, then we should believe that. However, Ramayana says, King Janaka found Sita in a furrow buried under the earth:
अथ मे कृषतः क्षेत्रम् लांगलात् उत्थिता मम
क्षेत्रम् शोधयता लब्ध्वा नाम्ना सीता इति विश्रुता | [VR - 1.66.13,14]
Later, when I was ploughing the ritual field then raised by the plough [from the furrow is a baby girl... since she is] gained while consecrating the ritual-field, she is named as Seetha, and thus she is renowned
So as there are no direct description of how Sita appeared under earth, other texts add up how that furrow ended up there. For example, the Sanghadasa's Jaina version of Ramayana says Sita was actually daughter of Ravana. When he heard from the astrologer that the first child would ruin his lineage, he gave her up and his men buried her in a furrow under the ground where Janaka later found her.
Regarding Vedavati, as per Skanda Puran she became the maya Sita whom Ravan kidnapped. Vedavati after giving up her life in fire due to Ravana's ill behaviour became Swaha, the wife of Agni. And when Ravana tried to kidnap Sita, it was Swaha who actually took the place of Her. So Vedavati was not the actual Sita, but the maya Sita.
Similarly, there are many other versions and stories. But when no authentic information is available, we should consider Janaka as Maa Sita's father. Because at the least, Janaka raised Her and as a parent wedded Her to Shri Rama. Even Mahabharat describes Sita as Janaka's daughter and says She was made by a rishi:
विदेहराजॊ जनकः सीता तस्यात्मजा बिभॊ
यां चकार सवयं तवष्टा रामस्य महिषीं परियाम [MB - 3.258.9]
Janaka was the king of Videha. Sita was his daughter. Rishi Twashta had created Her desiring to maker Her the beloved wife of Shri Rama
So there are many different stories and reasons. We just need to believe what the prominent texts like Ramayana and Mahabharat say.