I figured exporting the generated chunks in a vanilla world with the same seed would just make them have a harsh border at the edges but Minecraft actually cannot read the imported chunks and completely rewrites them

Did you have the height limit increased in the Tectonic world? The game really doesn't like the height limit being lowered.

Yeah it seems that was the issue, managed to circumvent that by importing sections 0 to 20 of the desired chunks with MCA Selector but wonder if there's a smoother process cause it glitched some part of the terrain

As far as I know, there's no smoother process.