Dear Tahir,
1. Yes, SAM calculates the incidence angle assuming solar noon at summer solstice.
2. Yes, the SAM ignores the IAM and end losses for the design-point calculations. The optical efficiency at design value represents collector geometry and other location-independent optical parameters (shown on the Collectors page). This modeling approach isolates the optical parameters that depend on collector design from those determined by location. Another approach that includes the IAM and end losses in the design value as you suggest would also be an acceptable modeling approach, but is not the one we chose for SAM.
Best regards,
Paul.