I had tried Handbrake for a week or two but found in far less satisfying than MediaCoder. And frustrating!
Handbrake was time consuming when working on a batch, each source file had to be loaded and “Add to Queue” clicked and, even then it often failed to convert all in the queue.
It's settings were ambiguous and not reproducible. For example, when aiming for an interlaced outut, I had set Anamorphic = Strict, as recommended for interlacing, and saved it in a Preset. However, on loading the Preset, Anamorphic appeared at its default value (‘Loose’).
Most important for me, since I require the max resolution for workimg in Premiere, Handbrake often failed to give the desired Resolution, which cannot even be set or changed easily. Handbrake has a mind of its own and usually chooses what it wants for the resolution -- usually lower than desired. It also seems incapable of convertig an NTSC file to PAL so that I can treat a number of clips on the same Timeline in Premiere.
For example, wanting to keep 720x576 for all clips, I converted 3 NTSC files in 720x480 to PAL:
The output framerate was correct at 25 fps but the two clips in 4:3 were output at 706x480 for one and 720x488 for the other, and a 16:9 source clip in 16:9 came out as 706x476. They all had a reduced resolution (quality) for a Timeline at 720x576.
I finally gave up using Handbrake. It may be useful for straightforward conversions but for me, NO!
In any case, MediaCoder lets you have control over everything you want and offers numerous other encoding options in case you need them.
That is why I re-examined MediaCoder and prepared the abovementioned Guide on Trimmed Versions (viewtopic.php?f=17&t=13044