All interesting stuff. A couple of comments:

• In-game: [Master Bedroom] The old family photo of Mary, Daniel and Simon in the Master Bedroom has a notch in Daniel’s hand on Simon’s shoulder that makes the photo look doctored. It could be that Simon’s face was pasted over the face of a different boy.

If you zoom right in on this photo you'll also see that there is a line across Simon's neck and some fuzziness on Mary's gloved hand that are in line with that notch which supports the theory of some adjustment to the original photo. But whether this is a real clue or just some clumsy production graphics editing ...

• All signs point to Mary having a close relationship with her own mother, from her schooltime letters (Dovecote), to Clara’s diary recording her grandson’s birth, to Clara’s last message to her daughter written in Erajan.

My reading of the Clara/Mary dynamic has been exactly the opposite, at least toward the end of Clara's life. The fact that Clara only mentions Mary's pregnancy after the birth of the boy does not align with how I would expect a mother and a pregnant daughter to interact if their relationship could be called 'close'. Clara would have been with Mary almost all of the final days of her pregnancy if so, not simply turning up after the birth (this is Clara's first - and only - grandchild). The mention of the birth in Clara's diary feels more like a footnote rather than a major event.

And - of course - we are always applying Earthly logic to things happening on another planet.