to build centralized systems upon a decentralized system, but not the other way around
It depends what do you mean by "centralized" and "decentralized". I can imagine a scenario, where all coins would flow inside the Lightning Network, then all on-chain transaction fees could be gone, and then guess, what will happen next: you will have a system that will run out of coins. Miners will mine all 21 million coins in circulation, and what then? No new coins, so the basic block reward would be zero. And then imagine that all coins could be locked in some LN channels, and stay there. If so, then miners will stop mining (because of no incentive), and then the whole chain will stop, because the whole life will be present entirely in some lower layers.
So far, the Bitcoin community has no solution for the scenario, when the basic block reward would be zero. Then, doing chain reorganization would be profitable, just to get some coins from the fees of the previous block. That means, this could be the way to disincentivize miners to extend the Proof of Work chain. And then, if no solution will appear, everything will be handled by the Proof of Stake.
Are there any downsides/benefits in doing that? Im just getting into how exactly lightning works at the moment and didn’t go into merged mining yet. Does someone have any good resources to catch up?
It is just an idea. If Merged Mining is possible, then something that I described, could be named "Merged Signing", so it is exactly "a scenario in which miners would vote out their own business model", because then it is possible to vote for anything, just by signing some transaction, and it is possible to prefer that, instead of using Proof of Work to mine blocks. You can always sign a transaction, and then it goes into staking. If you will look inside the Lightning Network, you will see, that there is no mining. So, how to name that consensus, that is inside that network? I would call that staking, because everyone can open a channel, and put all coins at stake, and then take profits from keeping some node online, and signing messages. There is only one difference: it is running on top of the regular Proof of Work chain. But I think it could change, I described the reasons above.
When it comes to the resources about Merged Mining, then see how the NameCoin works. And imagine that instead of reusing some Proof of Work from another chain, you could reuse a signature. Then you will get, how Merged Mining could work in a Proof of Stake consensus.