The 2005 log does include the mileposts less than 1.79, and it states that that segment was transferred to the city of Flagstaff in January 2005. The zero milepost is listed as "Begin U 089 at SB040(4)", and there is a point at MP 0.32 that reads "(EB) SB040(4) NB(on)", which reads to me like there's a brief concurrency with Business 40 before that splits off back to I-40. Mileages outside Flagstaff are the same in both the 2005 and 2013 logs.
Interestingly that 0.32-mile figure is a little bit off from what I'm measuring on Google Maps, but a detailed mileage analysis there is difficult because that junction has been significantly reconfigured since the 2005 route log was made - it was reconfigured from a full trumpet to a standard intersection in 2007.