Not sure how hard this would be, instead of running "flake8 blabla", one can run "docker run bla bla". Or even docker exec bla bla if you have the container already running. And by "you run" I mean vscode does that for you, via an extension.
It has support to use a a particular interpreter, specific virtual env, or it lets you say “my interpreter is inside this docker container”, which is even allowed to be on a remote host (although I’ve always used docker running locally).
They did a good job but it doesn't seem complete yet.