It's entirely possible Sakuya's time-based abilities come from her pocketwatch.
Also, as mentioned, "You've been with us so long that it doesn't seem fitting to call you human" seems to blatantly make note that Sakuya's been alive much longer than she seems to have been. The immediate next line, also, implies that the next in line to serve can be trained to do so. Not necessarily that time powers come with it, but it's a probability. If Sakuya were simply a human she probably wouldn't innately have such powers, either. But that's all speculation, I suppose.
I'm still of the belief that Marisa is gradually succeeding in her attempts, otherwise the whole point of making her "want to become long-lived" would be, narratively, redundant. She has to be succeeding at some level or else it would just be silly. Likewise, as there probably will never be a definitive end to Touhou, Marisa will also never achieve that goal within the span of the series. At (narratively) best, a work will pop up in the future, describing a future, where Marisa has indeed succeeded. At best best, it would be a passing mention of almost nothing. But if were to happen within the series it would be kind of lame.