Regarding your point of 'Also, if I look at ePWMA and ePWMB panes setting, is there a mistake for ePWMB output pane -- should CMPA on up-count (CAU) be set to Do nothing instead of Set?' the configuration for CAU field for ePWMB is independent of CAU field for ePWMA. So this configuration on one output will not impact output.
And going by your model it is very likely that since you have used Simulink 'Sine wave' blocks, it will generate code that is not optimized for embedded applications. This can result in overrun scenario as you clearly identified. We encourage you to use TI Math Library to generate the Sine values.
The following link provides some insight in to the same.
To interface to external C/C++ code from Simulink, like in this case you will need to call the Sin() function from Math library, please following the link:
You can also quickly do the real time execution profiling of the generated code by following link: