This is intently spooky and I quite enjoyed it. The aesthetic is impressive, the subject is gruesome, the writing is evocative and intriguing. My only wish is that there was a third stage of body exploring, but that doesn't detract from the overall quality.
I didn't play that educational game you mentioned, but I played games like it, and you've nailed that feeling.
Spoiler thoughts below this line...
As a huge fan of body horror and spooky psychic stuff, the Flowering is an excellent concept and reading about it got my imagination sparking. Rotting bones becoming delicate psychic latticework? *chef's kiss*