I'm not a programmer, and I recognize that you are. However, whenever Renee suggests that an RM user run the tools, she always says, "Run all tools in order." That would appear to be the official recommendation from the Roots Magician.
Reindexing is helpful in many work sessions, in order to keep the Sidebar Index fully populated with dates.
Removing phantom records seems to be a good idea when merging records as research documents links to orphaned individual records.
Is there any harm (besides the time required?) to running the Database Tools frequently?