As Shay's Rebellion was a decade after the Declaration of Independence, the earlier drafts could not possibly be referring to it as "domestic insurrection."
Jefferson must necessarily be referring to something that happened before he started his draft.
We are talking about the Federalist Papers, which appeared over a decade after the Declaration of Independence.
The question was what people in the late 18th century understood by the term "domestic insurrection."
In what circumstances would they use the phrase?
That would provide a clue as to how people understood the phrase when they read it in the Declaration.
Whatever private meanings phrases may have had in Jefferson's mind can't be recovered and probably don't matter.
Go back under your rock and ponder.