Unfortunately there is no definitive list of commencement orders that I could find. A Member of the House of Lords had better luck in 2010.
It seems (I am not sure) that Sections 39-41 of the Borders, Citizenship and Immigration Act 2009 have not yet been commenced, hence the "Prospective" tag on them on the Legislation.gov.uk website.
In any case, your father's application should be protected under Section 58(9)-(11) of that Act, which exempts people who already have ILR from the application of these provisions for two years after the commencement of the sections listed above.
This is a completely different requirement. The requirement to be physically (and legally) present in the UK at the beginning of the five year period is a requirement of Schedule 1, Section 2(a) of the BNA 1981 and has been a requirement since 1983. That only requires a continuous legal (Section 2(d)) presence of five years. Such legal presence can include a period under a visit visa.arbi580 wrote:What I don't get is there are various posts on this forum citing Section 2.3 of ANNEX B to Chapter 18 of British Nationality Act 1981 states that all he needs to do is be physically present in the U.K. for the 5 year period (3 year in case of spouse) and various people stating on this forum that they have been naturalised using their visit period.
I hope that clarifies matters and eases your mind.