Does the Bitcoin system still work with the design declared as manifesto?
No. Some things have naturally fallen away due to technology and experience.
In its overall design theory, it still functions well.
Have any design or structural changes been made on the system?
Not major changes, that I am aware of.
The whitepaper is a very simplistic outline and many things are
different now compared to 2009.
Who decides the changes to be made on the system?
The Validator Node Network in conjunction with the Miner Nodes.
According to what criteria do they make their decisions?
If a proposal receives a majority of approval signaling, then at a certain point in the
future whether manually or automatically, majority agrees to switch to that new change.
That is the current Consensus mechanism for "changes".
Does the developers have the authority to make such changes on the system?
No, Developers only propose different ideas and possibilities.
The Validator Node Network and Miner Nodes make the changes.
If the nodes don't like a proposal, they do not support it and thus no change occurs.
Do they get the idea of BTC users when making these kinds of decisions?
Developers do not make decisions, they propose different ideas and possibilities.
Decisions are made by the Validator Node Network and Miner Nodes.
The change only comes about due to their Consensus.