No. They are entirely separate documents. The Master Rule 12.0 PDF applies to standard Yu-Gi-Oh! (40 cards, 5 monster zones, 8000 LP). The Rulebook 2.0 (Speed Duel) applies only to Speed Duel events.
No. The Speed Duel format does not use Extra Monster Zones. Fusion monsters and Synchro monsters (if released in future Speed Duel sets) go directly to the Main Monster Zones. Yugioh Rulebook 2.0 Pdf
If you are used to playing the standard TCG, the Rulebook 2.0 will feel like an alternate universe. Here are the six key differences explained. 5 monster zones
This reduces the complexity of combo-heavy link and pendulum summoning, making the game feel like the Battle City era. Yugioh Rulebook 2.0 Pdf