Handbrake will re-encode entirely, not only wasting time, but also dropping the quality.
Let's not forget Handbrake: 1)provides a large reduction in file size, 2)will convert those BR's that are not natively h.264, 3)creates a reduced bitrate file that streams easily (quickly) over wifi, 4)converts DTS to AC3, and 5)produces negligible quality reduction when encoded using appropriate transcode settings.
But yes, the price you pay for those benefits is transcoding time, the amount of time depending on the processor used. Also, transcoding is easily can easily be done overnight using it's queue.
Whether you repackage or transcode really depends on an individual's situation, e.g. storage space, wifi vs ethernet, need for portability, etc
By the way, I do like MP4Tools and Subler. Both excellent products.