A normal Japanese person: "I feel like baking bread. Damn, I'm out of yeast. Gotta go buy some from the store."
A light novel author/mangaka Japanese: "I feel like baking bread. Alright, I need to extract a suitable yeast strain from these fruits I've lying around, and maybe then I can start baking, a few days from now with any luck."
This author is one of the foolish ones who can't come up with anything better than pretending ancient inventions aren't present in a world that looks like a weird mix of 17th-19th century Europe. The only saving grace is that this isn't an isekai where a Japanese person would graciously bring mercy and civilisation to hairy barbarians.
It's not like she invented yeast, she found a recipe in a book for a special kind of yeast. Also it's not like they claimed they don't have yeast, they just haven't been using that specific alchemically produced yeast. They didn't say anything about what they normally do to make the bread. Berries commonly have yeast and other things growing on the outside of them, and are a reliable source of yeast. However that's not among the most common historical sources of yeast for baking, it was more common to use a sourdough starter or various byproducts of brewing.
You need to reread the chapter. The text definitely made it sound like yeast in general was a previously unknown thing to the household. It's not due to the flour they use either, since Daisy did nothing but added her alchemy yeast to the mix. They have been basically eating what would be a failed bread so far, that is, if you are trying to make bread normally but your yeast is dead, yet you still push forward even though there's no leavening. You end up with quite miserable bread. But that's what those folks, apparently, have been eating all along.
"Did you just say soft bread? That's really unheard of." <- Yet they still use flour suitable for it. So, no leavening existed so far.
"Don't forget to teach me how to make yeast next time." <- No mention of this particular type of (magic) yeast, just yeast. Period.
