I could see lots of reasons to do software encoding at a company like Facebook which are probably not mentioned in the article, including e.g. extracting the optical flow which can be reused as part of various machine learning workflows.

For example, if you want to only annotate 1 in 100 frames and interpolate with optical flow, you can get the flow in the process of doing video compression.

I don't have inside info but there are various other things like this that I can think of for wanting to do it in software.

Also, hardware encoders suck if the company making the hardware decides to suddenly EOL the product. With software encoders you can easily scale the backend whenever you want, at any time in the future, and without succumbing to supply chain issues.