I believe it already is. I know that Create React App’s react-scripts component integrates this: https://www.npmjs.com/package/pnp-webpack-plugin
This is one of the nice things about just being able to use the command flag in CRA for PnP.
As for when that support will just be built in Webpack, I suspect it will need to be on by default in Yarn or potentially never. I can’t see them building in support until there’s a unified standards.
As for IDEs I admit I don’t know much about them as I primarily use Visual Studio Code and don’t really use anything that would be considered an advanced IDE feature.
Remember that Yarn is not as big as NPM so there will be more lag in it being added to support for anything. NPM seems to not being attempting to PnP(it’s a standard not exclusive to Yarn) to their own package manager.