1.Why there are only 5 skills that i can work on at the time? 

The workouts function in a block periodization structure, where movements are practiced and perfected in 2-4 week cycles. When working on no more than 5 skills at a time, more progressions and exercises for each can be executed. More progress will be made on strength and technique when focusing on a fewer amount of skills, even if you take 2-4 week breaks from those skills, then would be made by working on 25 different movements simultaneously. 

2.How long should I be working on each skill? (eg I have 5 main skills I am working on - how long is it effective to work on them before switching to different skills? Or should i just work until i will achieve them? - how can i use/ implement periodization for the most effective results)

Skills are trained in 2-4 week periodization blocks. You can choose to work on movements for more than one block if you have specific goals or feel that you are very close to mastery. 

3.Why there are Main and Side Skills? - what’s the difference? 

Main Skills are the movements considered essential to the world of calisthenics. Side skills are interesting movements which can be pursued if desired but are not part of the most important building blocks of bodyweight training.