We currently use the master branch to compare upstream / incoming changes to our customizations. This branch should have minimal changes required to run our modified applications, and no changes that do not exist across all our flavors.
What should be reflected in the master branch? The default for our branches OR the current state of the upstream master?
In general, if it's a change that would logically exist across all our flavors (ref, demo, and b2b), use that. This rule will make it harder to track deletions over time, but it's far more likely upstream will have additions than deletions.
The vscode extension Git Tree Compare is great for comparing magento/master to pmet/master and then pmet/master to pmet/pmet-x.x.x-[ref|demo|b2b|blank].
Once all upstream changes are merged from the upstream master to the our master, rotate thru each flavor to propagate each change while also looking for shared changes that should be in our customized master for all flavors.
A common workflow it to checkout each branch that may need to be updated and then change the base version in Git Tree Compare to the revelant repo / branch with the updates.