Short answers, pulled from the story.
Napoleon held the title Protector of the Confederation of the Rhine for the Emperor of the French. Article 12 of the treaty text explicitly states that His Majesty will be called Protector and can appoint the successor of the prince-primate after every departure.
The ratification of the Confederation Treaty occurred in 1806. This document created the title Protector of the Confederation of the Rhine for the Emperor of the French shortly before the lithograph by Charles Motte from the 1820s captured German princes rendering homage.
France alone decided when to mobilize military forces under Article 36 of the agreement without consultation required from allied German princes. The power balance remained one-sided allowing Napoleon to use the Confederation as an instrument to secure military support from Rhenish states when necessary.
Member states Westphalia and Berg ceded territory to France during 1810 and 1811. These actions breached Article 8 which stated sovereignty could only be declined to other Rhenish states while France acquired land despite not being a member of the Confederation.
Napoleon's defeat in 1813 led to the dissolution of the Confederation of the Rhine. The political experiment lasted only seven years before collapsing under military pressure and failing to guarantee long-term stability for member states.