Why must there be a clearance hole and pilot hole joining two pieces of material together? Why can't you drill a straight hole into them?
Usually you need a clearance hole so that the screw literally clears the first piece of wood and doesn't hold on to it. This is to prevent a problem called bridging where the screw acts like a bridge between the two pieces of wood, holding them apart. When this occurs no amount of tightening will bring them snugly together*.
More on conventional woodworking screws, pilot and clearance holes in this previous Answer.
*This can be resolved however — as long as the screws haven't been over-tightened leading to damage of the walls of the pilot holes the screws can be withdrawn, clearance holes of the right diameter bored and the screws driven back in. With luck this will result in the screws holding just as strongly as if proper clearance holes had been drilled initially. If not then see some of the tips given here under Loose screws.
While "bridging" can be an issue, it can be resolved by having the member clamped or forced together in an alternative way such as standing on the members. The prevalent use today of deck screws and "drywall screws", for purposes other than drywall, testify to this. In these cases, at least in softwood, either a single hole is drilled or no hole at all.
However, these screws are different than traditional wood screws which have a non-threaded shoulder. If you drill only one hole, especially in hardwood, this shoulder can cause significant binding while screwing in. If you accomodate this by making a larger hole, you compromise the ability of the threads to grab. Ergo, the two-hole solution.