The "Deploy to Hardware" should work fine with both CH340 and ATmega16u2 clones. For most of the Arduino boards the External mode baud rate is set to 921600. I have observed that CH340 cannot handle baudrate greater than 230400. This is the reason that External mode fails.
There is a hidden API to change the default External mode baudrate. Open the model. Check the default External mode baudrate by executing the below command:
>>codertarget.arduinobase.registry.setBaudRate(gcs)
If you want to change the baudrate to a lower value say 230400 then use: >>codertarget.arduinobase.registry.setBaudRate(gcs,230400)
If you have an issue with External mode even after setting External mode baudrate to 230400 then keep lowering it till External mode works.
Ideally the clones with ATmega16u2 that use original Arduino drivers should work seamlessly in External mode. I have not yet tested though.
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