On a Revenue Arrangement record, the Revenue Element sublist has a

Source

column, which contains a link to the Sales Order that generated the Element. However, the value stored in this field (for workflow/scripting purposes) is an internal ID that doesn't match the internal ID of the Sales Order. Anyone know what that internal ID would represent?

On my arrangements, the Source does reference the source document's internal ID (e.g. Sales Order, Credit Memo, Invoice). Are you getting your data from a report/search?

nope