Ok so I ran into this exact thing last month and it drove me NUTS until I figured it out. The lined basket holds heat way better, so your dough proofs faster and the crust sets quicker, which gave me a tighter crumb and a softer outside. Bare basket lets all that heat escape, so the bread takes longer to cook and you get a thicker, crunchier crust, but the inside can end up a little denser if you are not careful. What worked for me was sticking with the lined one for anything with a soft crust and going bare only when I wanted that hard bakery style bite. Also check your dough weight, because I was loading the same amount in both and the lined one was clearly happier with a slightly bigger batch. Try it side by side one more time and watch how fast each one browns, that was the real eye opener for me.