I am not aware of a way to have a story span multiple workbooks but I have dealt with a situation where I have multiple workbooks with dashboards that relate to a single theme or department. For example, dashboards and worksheets that are Admissions related but are in separate workbooks for the same reasons you state - overly complicated data joins or other considerations. In several cases like this I have created what amounts to a dashboard of dashboards - essentially a dashboard driven from an excel spreadsheet that contains labels and links to the specific workbook dashboards that I want to see combined into a common navigational view. I created a workbook that has a dashboard with 2 areas in it. On the left is a navigation panel that has links to the workbooks that I want as part of the theme and then a large fixed area to open the workbooks into when the links are clicked on. So for you you could have on the left several Stories listed and when each on is clicked on it would open into the larger window. You get all of the features of the standalone work book but in a common context essentially bringing the workbooks to the user, not forcing them to go to them. One of mine looks like the following where the workbooks you want to get to are on the left and they open on the right. Not exactly what you are looking for but it might be of use in certain situations.
I have a similar question. However, I found out that Tableau Story can take also "Dashboard" (not just from worksheet) in its main window. As a result, it should be able to achieve what you want (and I want): having two or more visualizations in one story point, as long as we have several dashboards to make several story points to become a story.
It seems Tableau Story can be more complex than its Dashboard. But if I want to contrast different time points, then I need several dashboards, and it may also imply that I need to create different worksheets for my different dashboards.
I have not constructed my story in that way yet. I have to carefully construct my story line first.