Some options like clangd.arguments don't have the correct scope set.
For example, when using this setting in .vscode/settings.json in a workspace, vscode shows the following error:

Looking at the clangd arguments in htop however, shows that those clangd.arguments are applied just fine.
(clangd.path for example doesn't give this error in this context.)
(This error prevents usage of the vscode.workspace.getConfiguration api as seen in espressif/vscode-esp-idf-extension#1619)