Sometimes a company will charge a dollar on a credit/debit card to verify that it is a legitimate card, then that dollar will get refunded after a few days (depends on the cardholder company).
As for shipping, amazon doesn't store things in non-amazon warehouses. If it doesn't say "sold by amazon" under the title, then it is being sold by a regular person or different company, not amazon. These people are just using amazon to sell their goods the same way people use ebay to sell things. Anybody can sell their items through amazon for a fee, a bit higher fee if you want it stored in an amazon warehouse as well (it will say "sold by xxx, fulfilled by amazon" under the title on the item page)
As for shipping from one amazon warehouse to another, would you rather pay a higher shipping charge to get it something mailed across the country or save money to have it mailed from your neighboring state? Often times amazon will move stuff from one warehouse to another (and it's by the truck load, not just a few items) to reduce shipping costs and to combine multiple items in one order. Would you rather pay for shipping for each individual item from different states?