Software v. Hardware Transcoder

Is there any discussion on the benefits of software v. hardware transcoder?

I am currently using hardware transcoder on an iMac and watch on the web viewer and Appletv. Everything seems to work well but I am unable to see captions on the web viewer. I read this is due to using the hardware encoding.

Is there any disadvantage to use the software transcoder in order to get captions on the web viewer?

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