Perhaps more bikes are coming with clips and straps than in the recent past, but certainly the high end bikes are still shown and setup without pedals. The shop will throw on some cheap composite platforms so you can test it and take it home, if you'd like. In the less expensive road bikes, there's a greater chance that the new rider doesn't have clipless pedals and shoes. Clips and straps are still a step up from composite platforms, and would be seen as such by the new rider, so it's seen as a plus. Unfortunately, the pedals are still composite as are the clips. I prefer clips and straps, and the metal ones I wanted on my new Specialized Roubaix were about $40 extra IIRC.

Pedals and saddles are too personal and are likely to be swapped out regardless of how the manufacturer guesses in outfitting the bike. I don't want to pay for upgrades I'm going to swap out anyway. Not that I know anything. I'm the moron who recently bought a CF bike and then replaced the CF seat post with an alloy one and mounted a seat post rack and a 29-year-old leather saddle on it.