I'm pretty new at building datasets, but I don't see System Notes as a related record to a lot of the common records I'm trying to report on. Is that the case? I can only report on System Notes if I start with them? If I start with System Notes, then I can't seem to include fields from the originating record. Saved searches let us link to related system notes for most records. Have I missed something?

That seems correct to me. You can join the system notes together with a transaction dataset in a workbook to get a better view

@Mike Robbins There exists a table known as a “transaction audit log.” If there are any discrepancies, you can revert to your original plan.