I haven't been able to obtain any from Hundred Hole Cave and I'm not sure where Basilisk Mountain is...?
Viewing post in Legend of Door ~Gale Wings~ comments
To clarify, yes, it’s possible to find a Crystal Flower at Hundred Hole Cave in Mt. Guido. However, you have to read the relevant book at Achstan’s library first, which requires an A-Rank Hanger License and finishing Gore’s quest to access the area beyond Acquia. Basilisk Mountain is another option, but it’s only available very late in the game.