Right, the default XSI layout assumes you have "always on top" turned off.
But people tend to forget that XSI has one of the most customizable interfaces around. You can adjust the placement of everything, and create a series of custom workviews you can switch between for different tasks. For instance, I have layouts (all of which make room for the taskbar) for full-screening the 3d window, two for texturing, modeling, and animation. They take no time to build, and let you create custom buttons to switch views from within a layout, as well as create custom toolbars specific to your needs.
Try checking edit->layout. This puts your screen into a layout editing mode. Then choose edit->new layout, and select the new layout as a copy of your old one. Now you can delete toolbars, add tools, customize views, divide the screen however you want etc. It's very cool once you give it a try, one of the cooler and often overlooked things about XSI.