Hi Caroline! It's unlikely that the lid being on was the cause for a flat top, though if it was domed when it went into the oven and flat when it came out, that's a sign that it was over-proofed. Shortening the rise time would help prevent that. A nice tight shaping like the one in step 6 here also helps create a higher rise. A 4 qt Dutch oven which is what we bake with can easily hold a loaf made with 3-4 cups of flour which is about a 1 1/2 - 2lb loaf. 

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