You can technically make it do that in your Window Layout, by adjusting the main Region to be about 40 pixels smaller (40px is the size of the Windows 7 taskbar by default, I believe). I will have to make the layout generator include layouts that avoid the taskbar area, for the drop-down box in the wizard. Without generating it most people will end up with mismatching aspect ratios on their windows

Here's how you can make the Window Layout Wizard or Quick Setup Wizard leave space for your taskbar, right now:
1. Get to the wizard screen with the generated Window Layout styles to choose from
2. In the properties box to the right, there is an option that says "Use Monitors" under multiple monitors at the bottom. Select it.
3. With the Use Monitors option selected, you should now see a "..." button to the right of where it says "(Collection)" on the same line. Click the ... button to bring up the monitors editor for the wizard
4. The monitors editor should now be up. On the left is a list of your monitors, you can switch the order around if you happen to want to change which monitor the generator is using as the main screen or whatnot (select the one and click the Up arrow). On the right side is the properties for a selected monitor. The "RectBounds" field is what will be used by the generator for that particular monitor, and will start out as the full resolution of the monitor. The "RectWorkingArea" field is the "Maximized" size/position for this monitor, i.e. everything excluding the taskbar. Set the RectBounds field to be the same as the RectWorkingArea field, and click OK.
5. The monitors editor should now be closed, and the preview will be updated with a smaller looking monitor, and the drop-down box of styles will now have a set of styles that does NOT overlay the taskbar.
... I'll be cutting that down to a single on/off option during the wizard, but that will set you straight until then if you need!