Maybe. It looks to me when Reg 14 was amended to introduce the £96 fee for prior approval of larger house extension (14.1zab), the amendments also includes a cross refer back to the exemption in Reg 4 at 14.1b.
Fees for certain applications under the General Permitted Development Order
14.—(1) Where an application is made to a local planning authority for their determination as to whether the prior approval of the authority will be required in relation to development under Schedule 2 to the General Permitted Development Order (permitted development) a fee shall be paid to that authority of the following amounts—
(zab)for an application under Part 1 of that Schedule relating to development permitted by Class A of that Part (enlargement, improvement or other alteration of a dwellinghouse) which exceeds the limits in paragraph A.1(f) of that Class but is allowed by paragraph A.1(g), £96;
(1B) This regulation shall not apply to impose a fee in relation to an application of a type described in paragraph (1)(zab) or (zac) (“the approval application”) where the local planning authority to whom the approval application is made are satisfied that the application relates solely to operations referred to in sub-paragraph (a) or (b) of regulation 4(1).
https://www.legislation.gov.uk/uksi/2012/2920/regulation/14
