The Initial SQL setting supports DDL statements such as CREATE TABLE, INSERT INTO, etc. Any results from these queries will be ignored. In contrast, the Custom SQL connection only supports a single SELECT statement and it must produce a result set.
I think the only ootb options is to create two separate data extracts and then blend them at the visualization level. If you need a tool to help you quickly build multipass sql queries including data blending checkout https://www.veroanalytics.com.