The question I have is that when the keyboard comes up, there is a small clear bar that appears under it. I’ve tried checking this in various other programs and it holds true there as well, except safari. Is there any way to either remove this bar and extend the keyboard itself or at least recolor the bar so that it blends in?
I just don’t like the feel of how it is done.
Update
I have included the picture of the keyboard in the calendar app where it shows the clear area.

That’s a user controlled setting: you can move the keyboard up and down by holding down on the “hide keyboard” button then dragging. You’ve probably done that by accident and the iPad has remembered your setting.