If You have multicams & external audiorecorders, it’s a good practise to let them roll uninterupted until the scene is recorded. Like if You record a koncert, it’s a hazzle if someone is using the start/stop button and creates loads of clips to sync.
It’s way easier to just have to sync the begining of each scene, and then do the cutting.
With that huge amount of pins and the minimal amount of time in the film, why not just make a simple transition between two pictures, one empty and one with markers.
With a new plug-in, You’ll end up with hours before it’s set and done anyway.
I suppose You can just blend them together by tweaking the transparancy a bit. Or maybe just using the built in dissolve transition. Hope I understood the question right.