When choosing settings for each of the building performance factors, should you always choose the setting that gives the absolute lowest predicted energy use?

Even though there is a range of options from least to most energy efficient, it's not always the best choice to choose the setting that gives the absolute lowest predicted energy use. One also has to consider the price. If the efficiency increases, but not a lot, then maybe the extra cost associated with it isn't worth it. It all depends on the utility.

How can you use Insight feedback to make design choices regarding materials, lighting, PV, etc.?

Insight feedback allows you to see how different materials or design choices effect the overall energy performance of your building. For example, you can see how different operation schedules effect the overall energy performance and the impact it has is dramatic. However, some things like roof construction, in my case, the "best" insulation didn't have such a large impact on performance making me believe that it wasn't worthwhile to increase the insulation value.

How can model-based quantity takeoff improve the design process?

How can designers improve their designs using the information provided by preliminary estimates of the cost of building their design ideas?

The model-based quantity takeoff lets you understand how much of each material your design would require. Those quantities can then be used to estimate the total cost of those materials. From there you can decide if the cost is too much and potentially change material types, or change the framing system.