"I would have had to go there eventually anyway to progress the story" - the secret areas, to my knowledge, don't require anyone to go to them to progress the story. Yes, they are the way to unlock certain mirage transfigs, but if they didn't do that, there wouldn't be much of a point to having the extra area. It's lke saying "Oh, I thought I found his cool secret volcano island in FFVII after finally getting my golden chocobo but it turns out I'd have had to do it anyway to get that materia." xD

I'm pretty sure I didn't find all the secret areas. I probably should.