Shouldn't we always use Web Optimized for Handbrake?
Solution 1:
If the video is going to be streamed, ever, then you should web-optimize it. This places a special block of the video file at the front called an "moov atom", which is sort of like a table-of-contents. Not sure why, but it is not at the beginning by default, and can appear anywhere. For Html streaming, this block has to be read first before the remote user can start viewing the video.
For a great medium-level explanation on this see:
http://rigor.com/blog/2016/01/optimizing-mp4-video-for-fast-streaming
Solution 2:
This is one of the reasons why not:
If you enable this and convert your video, the iPad will not play the video file! Instead you get the error "The operation could not be completed".
https://stackoverflow.com/q/24042894/1066234
Solution 3:
I guess this comes down to opinion. I always select Web Optimized but that doesn't mean that everyone would want to do that. Handbrake is open source software and I've discovered that it likes to let people pick what they want.
If you don't have a need for the web optimized additions, then why include them in the encode?