If you read the actual accord, it says Quebec controls the selection of candidates (CSQ), whereas Canada controls the admission process (PR).to limit or change the process in which permanent residents are allowed inside Quebec
Your link says the same thing: Quebec controls only the skilled worker program, and it can limit the amount of people coming to Quebec only through CSQ process. It has no control over the process of admission of PRs, in other words, once you have a CSQ, you might be delayed by the intake quotas. But unless there is any other reason why you are inadmissible, you will become PR.
"Canada shall admit any immigrant destined to Québec who meets Québec’s selection criteria, if the immigrant is not in an inadmissible class under the law of Canada.
Through bill 9, Quebec cannot influence the rules of admission of PRs into Canada. There will be no language test for CSQ holders, or permanent residents in Quebec. Is there any "buzz" about renegotiating the accord? I haven't heard it. And even if, nobody knows what will be renegotiated, so there is no need to raise fears unnecessarily.
BTW, you live and work in Quebec. If you plan to move out of Quebec becoming a PR, then go for express entry, but then you actually have to leave Quebec and live somewhere else eventually. If not, sit tight (and learn some french). That would be my two cents.