I had kind of a trouble with this for a couple of hours trying different alternatives but here is the approach that worked for me, it is kind of the same to this but with one extra step which is extracting the excel app scope sequence as a workflow.
so the solution was:
Use parallel activity with excel app scope as the first branch and every other click in other branches(generalize the selector to click multiple kinds popups with one branch if you can).
Extract every sequence you have in branches as workflows, so all of your branches will contain an invoke workflow activity.
Check the isolated property check box for all the branches other than the invoke of excel app scope.
Hope that’s gonna help someone.