I passed your questions onto to Barbara - the very talented weaver who designed the scarves - and this should answer your questions.
The colour order and threading chart on page 2 are how the loom is threaded and if you just follow this, then everything will work out perfectly.
To explain the threading notes on page 3:
If you look at the first ABA section on page 3, each A is 12121 and this is threaded LDDDL, and each B is 43434 and this is also threaded LDDDL. Drawn out in full, this "first" pattern section is ABABA - which gives you LDDDL five times. So, for each five thread unit, the two outside tie-down threads are light, while the two pattern threads for each unit, and the centre tie-thread is dark. This just gives you another way to check, when you are threading that you are getting the lights and darks in the correct heddles when threading.
Then the plain weave section is 13 ends all in Rust.
The centre ABA section has 13 units, and the whole section is threaded LD all the way across (1 chartreuse, I rust alternating for 65 ends total).
The plain weave section is 13 ends, all in Rust,
and the last ABA section is the same as the first.(LDDDL five times)
The threading notes on page 3 were just to act as a cross-check on the threading, but everything on page 2 is how the loom is threaded.