one of the most direct possible hints at scarecrow being connected to rio and tg jail is the fact that he speaks through the form of playstation symbols ㅡ tg jail can only be played on a ps vita. also if i remember correctly, tg jail was released right after the auction arc (in which scarecrow first made his appearance), as it transitioned into the rose arc and kijima’s introduction to the story (and ultimately, the transition of tg jail into canon).
rio/shikorae also speaks through the use of symbols (alt codes), so that might be another subtle hint at their connection.
@chiselian told me about the various endings in the scenario book in which it hints that kijima didn’t actually kill rio’s older brother and instead, kept him in an isolated warehouse. rio goes to the warehouse and although the scene’s description is ambiguous, it hints that there was another presence, alive (movement within the dark). i think this was also the ending that was titled “coffee for two”, where rio ends up having a cup of coffee with an unknown individual (his brother) at the very end.
midnight-in-town 