The drop down handle bars are easy to get used to, so I wouldn't be that concerned about them. You'll figure them out in one ride and they offer more hand positions than a straight handle bar. The problem with the Bike Direct bikes is that you will probably have to have them tuned by an LBS before riding them. As you intend to have a fitting done as well that may not be an issue. Check out your local LBS's before purchasing one on line though, they may have models in stock that would work for you and it would allow you to do a test ride first. I use platform pedals, Crank Brother 5050's, for my eight and a half mile commute from Maryland down through D.C. and have nothing but praise for them, but it's a personal preference of mine. You can get more power out of clip less pedals as they allow you to pull the pedals up as well as push them down. Saddle height to handle bars is also a personal preference and can be dealt with when you do the fitting.
Since you have time before you make your purchase, I suggest doing searches for Bike Direct and the specific bikes you're interested in here on BF. People on the forum are incredible generous with their experience and advice. I know there is a long thread on Bike Direct and debates just about every aspect of dealing with them and their products. Before obligating yourself to a Bike Direct purchase, look at other manufacturer's products as well. There are a lot of good bikes out there that will fulfill your need. I ride a Surly Cross Check which would be a purchase on the upper end of or exceed your budget, but it's a great commuter bike.