Hello @Ricky Schuleman - Thanks for reaching out, and posting on the MS Q&A.
Regarding:
Could someone please explain what these are for, why they aren't cleaned up automatically, and what is the recommended configuration/actions to control this behaviour?
As you've already discovered, the storage tables are mainly for storing Run History data and are named with the following format: “flows__[LANamePrefix][WorkflowPrefix][yyyyMMdd]__t000000z” and ends with actions/variables. By default, the retention period is 90 days, I believe, and should be cleaned up automatically afterward. As for control & what's possible with the data, the following tool may be of help: https://github.com/Drac-Zhang/Logic-App-STD-Advanced-Tools
Please "Accept Answer" if the answer is helpful so that others in the community may benefit from your experience.