I have read about some having nodes that are run by the users. Does such a capability truly exist and how does that help in decentralization.
It is possible. At one point in the beginning, bitcoin was run only by users with laptops and small computers.
But for most blockchains, users aren't forced to be validators (node operators) too. It's a choice.
Regarding centralized blockchains, there are various ways in which they are centralized. For example, all nodes are in a way controlled by an entity (as it happens on Binance Smart Chain). Or only a few stakeholders control what happens on the chain on a Proof-of-Stake blockchain like Ethereum. Or there is a big centralized entity dispensing funds discretionary on the blockchain, especially for development (many blockchains are in this category).
To be honest, I don't think there is a perfectly decentralized blockchain. There are various degrees of decentralization.