2. I advise trusting the Beersmith recommendation, which is based on key factors such as age of the yeast pack/vial (used to calculate yeast viability), original gravity and size of the batch. Homebrew shop recipes are simplified for a beginner. If you want a second opinion, check this out:
http://www.mrmalty.com/calc/calc.html. Sure, one yeast pack per 5 gallon batch of standard gravity wort will produce beer. But it will not be the best beer it can be.
3. In the default Beersmith fermentation/aging profile, "aging" refers to the bottle conditioning period. In my experience, 3 weeks is the minimum to achieve carbonation--more time required if the bottles are stored in cooler conditions. The flavor of the beer will improve with additional storage time (weeks/months).
4. The priming sugar recommendation in the recipe is based on the planned batch size, so it will not change based on measured bottling volume--but it should IMO. I suspect that the Beersmith recommendation in the recipe assumes that your final volume is close enough to your planned batch size, so the difference should not be meaningful. You always have the option of using the Carbonation Tool (available from the tools menu) to calculate a more precise amount of priming sugar. That is what I used to do when I bottle conditioned beer.