1) Step downs are more movement specific and mimic going downhill better than step-ups. Greater emphasis on balance and eccentric contraction under bodyweight + gravity.
2) Will defer to others.
3) I believe the theory behind the program design goes back to Sport Specificity. Squats (as found in the General Strength Routine) are probably the closest exercise to the deadlift and are likely used in-lieu of the DL because in the sport environment we recreate/compete in, the weight we lift is typically located above our hips vs. below our hips (as in a DL).
If you want to add in DLs, I’d say put them in so long as they do not take away from the rest of the exercises (i.e. reduce your capacity to execute the other exercises well). Watch your recovery and how the body feels. Deprioritize/eliminate the DLs if you find they are detracting.
4) Does casual cragging = climbing for fun = not projecting? I’d say if they’re easy days at the crag and you’re climbing lower grade pitches (whatever “low” means for you), put it in on a recovery day. But if your “casual cragging” includes projecting and exerting high effort, this is time and energy you may be taking away from other training days…you may need to re-evaluate whether or not cragging is contributing towards your goals.
Can you tell us what you intend to accomplish/pursue in using the 16 week program?