Something is off here. In the past 5 years of using the BIAB-VST I have never run into this issue.

I would agree this looks bad. Synchronization is critical in digital audio production and this seems to indicate things do not synch up.

After a bit of study, I feel the primary reasons I have not experienced this is in the BIAB-VST or BIAB when moving tracks to Reaper is my workflow:

1) I often have the "endings" box checked in the BIAB-VST. This totally eliminates this problem with the bars not synching. And if I don't want the ending, I would simply cut that portion of the audio in the DAW. [This is what I would recommend to the OP]
2) If I do happen to turn off endings (which I do at times), then I have never needed to immediately add additional audio following the track. So nothing has to synch with this track when it is done.

I concluded this issue as described is unique to the workflow. I have no problem with PGM adjusting this as long as they don't mess it up. For my workflow, this all works fine.