When asking about fairies, the flirt option never came up during and after the quest. Did I miss something?
As I recall, the time to do so is only available during the storyline when you are looking for a fairy for the guild, and you can only flirt with her if your reputation is high enough with Wimborn.
So best thing to do is spend several days saving travelers from bandits and not asking a reward right after you get the quest for capturing a fairy until Maple flirts with you. I also believe that each level of flirting requires a higher reputation.
I was curious, so checked the code. you're right, you do have to start it while doing that quest. However, you only have to ask about faries, nothing more. The flirting can happen later, asking about fairies starts it out and that requires the mainquest, but the rest is independent of that. Everything requiring reputation can happen at any point after that, so just make sure to ask her about fairies when first tasked with finding a fairy.