There are quite a few things that are difficult to believe in any religion and hinduism has its fair share.

Baaraha avataar is where the world is thrust deep into an ocean by evil entity and baraha avataar a wild boar pushes the earth back to the surface of the ocean.

Did the gods think that the earth was floating on top of a ocean?

 They were very smart to know that Boar ( wild or home) carries tapeworm and made up a story and made it as Bharah avatar. Brahmin and chhetri did not eat Pig.
So did Jews and followed by their cousin muslim.

There might be few flaws in Hinduism but there are extremely deep stories that science proves true today which is amazing. I don't get how hundreds of years before they had this tech but again I feel like this is just an era and everything's gonna end one day and we gonna start new era and talk about the one we live in.

So you were fine with grafting a boar's head on human body but had issue with earth being in a sea?
Kidding.

One can have various interpretations of what's written and you can find a version that fits the scientific model. Bhudevi, that Varaha rescued, could be just a mass of land - not the earth as a whole. Here's what Wiki says:


"The earliest versions of the Varaha legend are found in the Taittiriya Aranyaka and the Shatapatha Brahmana. They narrate that the universe was filled with the primordial waters. The earth was the size of a hand and was trapped in it. The god Prajapati (the creator-god Brahma) in the form of a boar (varaha) plunges into the waters and brings the earth out."

This fits perfectly with our understanding of Earth. 4 billion years ago earth was a hot rock. Earth was then covered with water until around 2.5B years ago.
While the timeline doesn't match (I think each yuga lasted about 1.5 million years), you can make a point that our forefathers knew land emerged out of water. The 10 avatars also follow the chronology of how life started in earth.

Kiddo baraha avatar was not about grafting a boar's head on human body but the supposedly divine existence taking form of a wild boar at birth and growing into a big boar. I know you were kidding but let's get the story straight :)

In my opinion it would be naive to believe it has any resemblance or connection with the creation of earth.