Just use workspace settings, in VS Code you have User settings that are used for every project, and Workspace settings (saved in .vscode/settings.json in the project folder) that are specific to that project.

If you want to share workspace settings with others you can commit .vscode/settings.json.

You can edit both settings directly on the .json files, or through the VS Code settings editor (Files->Preferences->Settings).

You can set the VSCode setting html.format.preserveNewLines to false. It will be recognized by Beautify, but works only for HTML files.

The alternative to apply the setting for all files recognized by Beautify is to add a file named .jsbeautifyrc at the root of the workspace, with the following content:

{
   "preserve_newlines": false
}

Also, the VSCode setting editor.formatOnSave should be set to true. To do it you can create the file .vscode/settings.json with the next content:

{
    "editor.formatOnSave": true
}

The settings.json file, located at the .vscode folder in the root of the workspace, allows to configure the VSCode settings to be applied for the current workspace.