Faces of the Maiden.

 

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The bottom face is 'Yoshiro' and this is when the Maiden becomes the abode for the Goddess.

Is it safe to say that the Maiden's face changes due to their intertwining/merging?

It's made visually clear that her face changed to resemble Soh once she became Yoshiro.

This face from the art is seen in the trailer:

Original face

Originally, Yoshiro's face was closer to Soh's face. It might've been changed to avoid confusing them to be the same person. But this change in her face absolutely should have been shown somehow in-game. 

It makes it very clear when that the Maiden becomes 'Yoshiro', she is merging with the Goddess.

And that this merge actually physically changes her.

In the final game, Yoshiro keeps her Maiden face:

Versus her first face, which is true to the art:

Here's Soh's:

Her 3D face seems prettier and less harsh.

A missed opportunity to show what 'Yoshiro' actually is and what's happening to the Maiden when she undertakes this duty.

I once said this face resembles Soh's:

Here she is becoming a vessel for the Goddess. It would explain her face resembling Soh's.

In the scrolls, I just noticed the 'Birth of the Goddess', this Goddess has her eyes closed:

I always thought she was looking down...but it appears not? Her eyes are closed.
The black in the middle is her make-up.

Looking at the scrolls again, are the Maiden's eyes meant to represent something?

Faces are definitely important in Kunitsu-Gami. Everyone is masked. Yoshiro wears a veil until her  petrification begins.

Only Soh gets to see her without her veil, in the tent. Oh, and the villagers who come to leave offerings for her.
(and Soh as they are seen as one in the same. It's why we receive the offerings.)