This app (like its counterpart MKVtools) is invaluable for remuxing a multi-language file, for example, keeping only the language you want, or for moving the content of such .ts file in a .mp4 container.
Comparing it to VLC or HandBrake, like the former commenter did, is a nonsense to me: I've been using both for years and they simply don't offer remux functionality (well, there's a way to kinda do it in VLC, but you can't choose which audio flux, and it's not as easy and efficient anyway).
I agree that the presentation of the app is misleading as it focuses on conversion but it's a lot different compared to most other converters.
Yes, if you strictly need conversion, use Handbrake!
In the case I mentioned above, I regularly need to remux .ts files to mp4 because then, if I want to sync subtitles, the utility I use doesn't recognize .ts files. Unfortunately, some streams I record have issues with their audio format and in such case I have to convert the audio track in MP4tools but without converting the video track!
I've been using Remux.app before, and it usually works ok but not always — and doesn't offer conversion, if needed. Another free contender is Subler, but I often had issues with it.