Please improve the subject line. Otherwise, people (including developers) will probably overlook it as useless when scanning through the list in the category at a later time. We are rarely going to try to fix a problem as soon as we read about it.
The problem is that Mask:Apply does not reset the alpha channel. That might be a feature for some, but a bug for others. You can see that by hiding V2 and adding a Alpha Channel: View after the Mask: Apply. The, track blender - by design - combines the alpha channels of each video track. The reason the Operation: Add makes a difference is because the Mask filters take a snapshot of the input image to be used with Mask:Apply, and the second Mask: Simple Shape’s input image includes an alpha channel. With the alpha channel view applied, you can toggle the second Mask: Simple Shape filter to see what I mean. The blender in Mask: Apply is alpha-combining as well.
The workaround is to reset the alpha channel on V1 after the Mask: Apply (or on the track) by adding an Alpha Channel: Adjust with Mode = Threshold, Amount = 100%, and Invert ON. I will add a Reset mode to this filter for the version after the next.