The new smart tempo multitrack sets have a feature whereby you can exclude specific tracks in the set from contributing to the tempo analysis. There seems to be a bug with this feature though. Unfortunately, it seems that it only writes the tempo info into the files that are included in the analysis and omits the files excluded from the analysis.
The problem becomes apparent if/when you turn flex on. The files don’t all get flexed the same, and the timing is off. There is a simple workaround though. If you open up the multitrack set in the smart tempo editor and move one of the markers in the downmix file, it automatically updates all the members of the set with the correct tempo info. And then voila, flex works consistently on all the tracks in the set.
I just added an additional video on this to the new groove3 LPX 10.4.2 Explained series today and asked groove3 to make it one of the free preview videos. It covers the workaround for this buggy scenario when using the new smart tempo multitrack sets and flex time together.