I agree: changing the bobbin should be easier. I love your idea of working "the other way". I guess you would have to decide the distance you want between the needle and the edge of your counter, and take it from there.
I quilt on a TL2010Q the "traditional" way. I have about 7.5 inches between the needle and the edge of the table. My machine is set into the table. Sometimes I think I would like more space between the needle and the edge of the table. But it's too late now to do much about it.
By the way, I think you'll love the Juki. I've had mine for almost three years. It's just great.