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Having just started using Portfolio I find it incredibly confusing. We have a very small team and so it is unlikely that more than one single team member will ever work on a particular epic. What my Portfolio schedule is assuming is that a team member would be happy to context-switch from one epic to another according to Portfolio's inner algorithm. The result is that all the epics appear to run concurrently but take several years to complete.
Is there a way to treat epics as an atomic unit that must be completed before starting items in another epic?
To schedule an issue so that it must be completed before another issue can start, what you are looking for are call Dependencies.
Setting up the dependencies is covered in here, and additional details on how the Dependencies effect the timeline is covered here.
By default you will have the Blocks dependency set up tied to the Blocks / is blocked by issue links. So as an example if Epic-1 Blocks Epic-2 then Epic-2 will not be scheduled to start until all the child issues in Epic-1 are complete and the epic itself is completed.