Is Transcoding to .MKV The Only Way To Keep Best Quality and To Be Able to Apply Time Remap Filter?

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1. That is normal.
2. Choose the “better” option, which is sometimes called a visually lossless if not mathematically.
3. It is not only MP4 files. The Time Remap lets you go in reverse, and when the video is compressed with B type frames the performance and reliability is too poor.
4. No, only ones with B frames. You do not need to fully understand video compression and B frames to understand and accept this condition, but you can search the web to learn more about compression in general.

See also the docs

Time Remap Filter

The Time Remap filter is the first filter that allows altering the timing of the underlying source clip. It maps clip time to output time. [image] Limitations It can only be added onto clips with NO B-frames. If you try to add it to such a clip, it shows the Convert to Edit-friendly dialog. A proxy clip can mask the above check for B-frames and then export may be very slow or give bad results. However, it may also be a very convenient workaround for the check and dialog mentioned above if you…