Can you guarantee that the completed building will match the performance predicted by the analysis in its day-to-day operations?
Absolutely not and I think Y2E2 is a direct example of that. This is because during the construction process, materials and features may not be installed perfectly as they are assumed to be in the model. They may not be as high quality as predicted and they may even need to be cut due to budget restrictions and downstream decisions to try to save money on the construction phase. In the US, this is common due to the long time scale of building projects, underbidding, etc. Thus, from the outset the building rarely perfectly emulates the model.
Day to day operations are also simplified, failing to capture the complexity of actual human activity and work especially in response to things like seasons, sudden technological disruptions, things like a pandemic that affect behaviors, etc.
When choosing settings for each of the building performance factors, should you always choose the setting that gives the absolute lowest predicted energy use?
No because often times such technology is more expensive and thus drives up the initial investment cost of the building. Higher initial cost may simply not be possible given the client's budget or appealing given the client's profit goals. Thus choosing the absolute lowest predicted energy use may not be the best choice especially if the change in energy use is margianal.
How can model-based quantity takeoff improve the design process?
As shown in my previous answers, budget and construction cost can really hinder the development of an excellent building. Thus, a model-based quantity allows developers to more accurately predict how a specific material and architectural choice together are influencing the overall budget. With the pairing of material and cost, designers can then make the choice early regarding whether they should use one material over another to achieve the same intended structural/experiential effect at significantly lower cost. Additionally, basing off a model allows the design to continue to lead decisions rather than just the flat numbers of a budget spread sheet.