As I read it, you're correct in saying that the relevant legislation only applies to persons who committed offences on or after 4 April 2005.
Provision for extended licences is provided by Section 227 of the 2003 Act:
http://www.england-legislation.hmso.gov.uk/act s/acts2003/ukpga_20030044_en_18#pt12-ch5-l1g22 7
It specifically states that it only relates to convictions where the date of the offence (not of conviction) is after the date on which Section 227 commences.
Section 336 states that Section 227 will only come into affect when a date is set, by Order, by the Secretary of State:
http://www.england-legislation.hmso.gov.uk/act s/acts2003/ukpga_20030044_en_24#pt14-l1g336
The Criminal Justice Act 2003 (Commencement No.8 and Transitional and Saving Provisions) Order 2005 states that Sections 224 to 236, of the 2003 Act, commence on 4 April 2005:
http://www.opsi.gov.uk/SI/si2005/20050950.htm
Chris