A1: They are used to extend the sides inward to provide an edge to attach and support the floor panel. Page 6 of the plans clearly shows them. You can also use fragmented scraps of 2×4 to serve the same function. They don;t need to fit exactly, just need enough to provide support for the floor panel. Hope that helps.
A2: If you lower the leveling feet, you can sometimes gain another 3/4 perhaps. If you buy something that needs a higher opening, just add the height to the bar vertical supports to suit your needs. This can be done either manually or using the CHBD.