You don't need to buy the racks, fenders etc. now. Those are nice to have, but not essential. For a 3 mile commute, any backpack will work fine until you save up the money for the accessories.
The advantages of buying your entry level commuter bike from a bike shop are that they already assembled it, and they usually offer free adjustments for life. That really helps out at first.
If you take your online bought bike to the shop, they will charge you full price for everything. Assembly will cost probably $100, tune-ups are about $100, flat repair about $10, etc.
That really adds up after a while, and makes your online purchase not as cost effective.