Previously, AVStream.codec.time_base was used for that purpose, which
was quite confusing for the callers. This change also opens the path for
removing AVStream.codec.

The change in the lavf-mkv test is due to the native timebase (1/1000)
being used instead of the default one (1/90000), so the packets are now
sent to the crc muxer in the same order in which they are demuxed
(previously some of them got reordered because of inexact timestamp
conversion).