That doesn’t matter. A Flow hive is managed exactly the same way as a traditional 8-frame Langstroth, just the honey extraction is different. If your locals use double deeps for brood, you should too. Only put the Flow super on top when the second brood box is at least 80% full.
Don’t leave the Flow super on over winter. You are right, the cluster may well leave the queen behind to die. If you remove the excluder, she may start laying in the Flow super the following spring, making a real mess for you to clean up. At the end of the season, harvest all honey from the Flow super, then remove the super. If the honey isn’t capped, freeze it to preserve it, and use it (defrosted) to feed the bees in the Fall. Even if all goes well with the Flow super on the hive, the bees tend to propolize the cells over winter, which makes it very difficult to open them when you next harvest.
When you do that last harvest, let the bees clean up the plastic. You can rinse out the collection channel if you like, but otherwise no vigorous cleaning is needed. Tightly wrap and then freeze each frame for 48 hours (kills SHB and wax moth eggs/larvae). Store over winter in a cool dark place (shed, garage, basement etc).