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Are you sure it's 720p? Or is it just 720 pixels wide?
If you were actually working with 29.97fps interlaced footage (not progressive as you said), you would want to go to 59.94fps in Handbrake (double the original), not 50fps.
The video link you posted has the other settings they used right in the title (deinterlaced decomb eedi2bob default). If your footage is in fact interlaced, and you want to mimic the settings used in that video, you would just select those in the filters tab. Then change frame rate to 59.94 constant. Pick a CF quality of 18 (or whatever you want). There are a few other quality settings and speeds you can select but that's the basic gist, to answer your original question, assuming your footage is actually interlaced (otherwise why would you be asking how to deinterlace it, right?)
I don't know why anyone would want to emulate that YouTube video to begin with. Just look at all the shimmering going on, especially of the railings on the right side at the beginning.