Because the Benn Act says that a letter requesting an extension must be sent if MPs have not approved a deal. Not just if no deal has been agreed between Johnson & the EU.
s1(1)(a)
1Duties in connection with the withdrawal of the UK from the European Union
(1)The condition in this subsection is that a Minister of the Crown has laid before each House of Parliament a statement that the United Kingdom has concluded an agreement with the European Union under Article 50(2) of the Treaty on European Union and a copy of the agreement and—
(a)the agreement has been approved by resolution of the House of Commons on a motion moved by a Minister of the Crown, and
http://www.legislation.gov.uk/ukpga/2019/26/enacted/data.htm
That says no such thing. If you think it does then a GE awaits, not another referendum.