Sprinkle chicken all over with salt at least 30 minutes and up to 1 day ahead (chill, covered, if more than 30 minutes).
Put ground saffron in a small glass or bowl with 2 tbsp. hot (not boiling) water and the rose water, if using. Stir to combine, then let steep 5 minutes.
Heat a 12-in. frying pan over medium heat. Add oil, then arrange onion slices in a single layer; sprinkle with a pinch of salt. Scatter garlic over onions. Place chicken thighs on top in one layer if possible (a little overlap is okay since they'll shrink as they cook). Sprinkle with pepper, then lemon juice, then saffron water. If any saffron remains in bowl, add a bit of hot water, swirl, and add to chicken.
Bring to a simmer, partially cover, and reduce heat to medium-low. Cook, turning a few times to coat in juices, until cooked through, 45 minutes to 1 hour. Season with salt and lemon juice if you like.
Lift cooked chicken to a cutting board. Holding each thigh steady with tongs, cut meat off bone into bite-size pieces. Meanwhile, reduce juices in pan over high heat to about 1/2 cup. Return chicken to sauce and set aside, covered, until ready to use.
Make ahead: Up to 2 days, chilled.