That article mis-describes what a mining pool actually is. You need to be careful not to confuse or obfuscate concepts without thinking it though a little deeper.
A mining pool consists of a large number of individual miners, who mine independently, but combine to share blocks when discovered (giving more consistent and predicable flow of income). This does not mean an entire pool could be coerced into a 51% attack. Indeed it would be virtually impossible given how many miners are in a typical pool of miners, and secondly because there would be no financial incentive to do so (indeed quite contrary to any financial incentive) to do so any individual miner. This is part of the beauty of the proof of work model. Every aspect of the ecosystem is incentivized through self interest, to benefit the strength of the network. So yes, a pool itself is "centralized" to the extent the share block rewards, but they consist of thousands of decentralized miners who act independently and in self interest. So, what you need to do is look at the power of each individual miner, and then bare in mind that new minders as constantly coming along, either to mine alone, or joining a pool. Think of a pool really simply as shared payments.
I'll give you a simple example. Lets say we have 9000 orange growers in the US. 4000 of those decide to join an producers collective - ie they all sell to a single aggregator who in turn gives a guaranteed price and is a consistent buyer. Does that mean that if the aggregator tried to order all 4000 producers to destroy their crops, that each independent grower would do that? Of course not. Why? Well because even though the "pool" is a centralized entity, it consists of many decentralized players. Indeed any smart individual grower would immediately would know that their oranges immediately become more valuable if others were to disappear. Classic economic game theory.
Mining pools actually incentivize more miners to enter the mining business, as they can get a consistent and immediate return on capital, and then grow without large outlay, due to the predicable and immediate shared income. As a result, they are a positive force to the strength on the network.
The second (and 3rd layer) technologies are built on top of Bitcoin, not into Bitcoin itself (but yes, it is correct that Bitcoin can be modified to be optimized for such 2nd layer solutions). This is core to the ethos and tenants of BTC. BTC, as open source code can be modified (and indeed is regularly tweaked). This is indeed because bitcoin is decentralized - it has no centralized leadership (unlike ETH, which can essentially be "selfishly" be changed to the benefit of those with larger stakes - which of course was the whole problem with fiat currencies BTC was designed to defend against, where some small minority in the financial system are advantaged over many others). Proof of stake on the other hand, is a perversion of the fundamental concept of a decentralized currency. All are not equal under ETH, On the other hand, all stakeholders in the BTC ecosystem are incentivized to ensure that any upgrades to the network are backward-compatible and its ultimately up to the community as a whole to approve of any so called "consensus changes" (the taproot upgrade being one such example). And any change to the BTC code inures the benefit of all Bitcoin holders in a proportionate and equal manner.
