For those who may stumble across this in the future, I have a solution to both issues. Ultimately I belive both issues are due to internal ActiveX/Excerl settings, nothing to do with MATLAB.
First, to have the workbook not prompt the user for Save/Do not Save, the following line can be used to "trick" the workbook into thinking it was saved. I have it a line before closing the application.
Wkbk.Saved = 1;
Second, and less elegant, but achieves the same result of the user not having the Excel window bombard their screen, I use the following just before opening the workbook:
hExcel.WindowState = 'xlMinimized';