This is not true. Washington, Madison, Jefferson were all considered natural born citizens in 1787. This is clear from Madison's discourse on citizenship on Smith's eligibility.
Anyone born under a Colonial government was a natural born member of that State, even though the State had transitioned from Colony to State.
And historians are in broad agreement that the purpose of the grandfather clause was not to provide eligibility for those born in America. It was to provide eligibility for James Wilson (born in Scotland), Alexander Hamilton (born in the Caribbean) and other foreign-born patriots who had risked their fortunes and lives to bring our country to birth.
Jefferson was born in Virginia Colony in 1743. How do you propose he was a natural born citizen of a country which didn’t exist until he was 33 years old?