Can someone explain to me how this notion of Marethari knowing less about the Eluvians than Merrill came to be? If the keeper is the one in charge of all the lore, how does Merrill have information that Marethari isn't privy to?
Because Merrill actually bothered to do research where Marethari didn't.
When Tamlen and Mahariel first found the Eluvian in DAO, every Dalish's reaction (Tamlen's, Mahariel's, Merrill's, even Marethari's) was "What's that mirror?"
However, Marethari went, "We don't know what it is, but since it apparently caused the deaths of two clan members it's obviously dangerous and therefore we shouldn't look into it further." However, Merrill's reaction (both in DAO and DA2) is, "We should look into it. It could be useful." Between DAO and DA2, Merrill looked into it and learned a great deal about what it was, what its uses were, and how to repair and restore it.
Exploring dialogue in DA2 reveals that Merrill pretty much single-handedly researched everything she could about the mirror, approached Marethari when her research was basically done, and basically said, "I looked into it, and I know what this is and how to repair it. It was the taint in the mirror that killed Tamlen and Mahariel, not the mirror itself. I also know how to cleanse the taint. If you help me cleanse the shard of the taint, we can get to work repairing the mirror together." But Marethari refused to listen to her, simply going back on the same broken record of, "It's dangerous! That mirror caused the death of our clan mates! We shouldn't mess with it! It was forgotten for a reason," etc, so Merrill took matters into her own hands. And again, she only asked the spirit to teach her blood magic so she could use it to fuel the magic needed to cleanse the shard of the taint, and from then on she used the shard to reconstruct a new Eluvian through regular magic and good old elbow grease.
Just because Marethari is the Keeper doesn't mean she knows more about the Eluvian than Merrill. Marethari's willful ignorance about the mirror compared to Merrill's willingness to research and rebuild it shows that being Keeper doesn't automatically make one inherently more knowledgeable about something than someone willing to learn.