"I can't use the stock I bought as collateral in the repo market right?"
In principle, you can. Repos can and do happen between non-government actors, with any AAA-rated paper being preferred, but a slice of the repo market does deal in riskier instruments like corporate bonds and equities. But that piece of the repo market likely isn't big enough to impact the money supply, and it isn't what's being alleged in the article you linked.
The article specifically addresses repo transactions between the Fed and financial institutions. In these, the Fed buys Treasuries from banks under an agreement to resell them at a higher price, usually (but not necessarily) the next day. The spread is the repo rate. The intended effect is to increase short-term liquidity, by inducing banks to reduce prime rates and lend more freely. This lending is supposed to support real economic activity that is otherwise not happening due to various frictions in the economy - it operates on the presumption that output is below potential, and that this is primarily because of credit constraints based in sentiment rather than fundamentals.
The issue is that if the market fundamentals have shifted so that the economy is in fact not producing below its potential (or not as far below as is believed), but is rather transitioning to a new and lower steady state, then there is no appetite for the liquidity being injected in this way. So while banks are enticed to sell off their Treasury holdings because of aggressively low repo rates, because fundamentals in the economy are weak, they are reluctant to increase loans to economic actors. Being bound to repurchase those treasuries in the short term, they pile the money into financial markets with the expectation of realizing their desired gains in this way instead.
Being collectively large enough to move share prices, when all of the banks are doing this together it produces a false signal: normally, markets rise because the underlying economic activity represented by stocks is rising. Yet in this mechanism, markets are rising even as the underlying economic activity is stagnant or even declining.
This is what analysts mean when they talk of "decoupling".