movenc: Don't assume that fragment durations in pts is equal to duration in dts

For strict CFR, they should be pretty much equal, but if the stream
is VFR, there can be a sometimes significant difference.

Calculate the pts duration separately, used in sidx atoms and for
tfrf/tfxd boxes in smooth streaming ismv files.

Also make sure to reduce the duration of sidx entries according to
edit lists.

Signed-off-by: Martin Storsjö <martin@martin.st>