Chin-ups will produce a different body shape than pull ups, and different muscular balance in your back. They're not THAT different, but different enough that if you do a lot of one and not the other, then switch, you'll immediately see and feel the difference.
I'd be prone to believe that GSLP has chins rather than pulls because it's designed, as others have mentioned, to be more comprehensive and fill in some gaps compared to SS or PP. GSLP has a more "lifestyle strength" and "appearance of strength" vibe going, rather than SS/PP's sole focus upon competitive lifts as a measure of strength. The difference in Chins vs Pulls is apparent for this purpose...
Deads will thicken the lats (front to back), and works on developing the length of the lat (top to bottom). Chins focus differently on the lats, with a broadening (side to side). Chins also build more at the base of the lats along the spine compared to pull ups. Deadlifts and pull ups will work more near the top of the lat near the spine (and base of the traps). Chins also focus the biceps more, AND more on the SITS muscles tying around your shoulder blades than pull ups, as well as hitting the brachioradialis and extensor muscles in a different way than any other lift in the program (ok, so switch DL grip hits ONE side in that angle - but it doesn't contract, it's isometric).
So yeah, it's fine to substitute, but I personally wouldn't 100% replace chin ups with pull ups.