You should probably consider raising your problem as a bug-report or feature request on our issue tracker. It doesn't read like a 'question' to me, and so it probably doesn't belong on SO as such.
Nevertheless let me try and answer as best as I can.
Even after adding the quickfix, the error is not seems to be going
It will, once you save the additional-spring-configuration-metadata.json
file where the quickfix creates new metadata for you.
I agree it is a little unintuitve that the change is not saved automatically, but I'm afraid we (STS vscode extension) don't have control over this. The changes are being applied by the Vscode language server client, and it's the client's decision to apply the changes only to 'dirty' editor buffers rather than apply them directly to the files on disk.
As to your general statement that 'In STS 4.0 ignoring unknown property support is missing'... I think you are referring to the fact that in STS3 it used to be possible to ignore problems of a given type altogether and this is no longer possible in STS4. This is true. If you like to get this kind of user-configurability back again, please consider raising a feature request on our issue tracker. SO, really isn't the place to ask for this sort of thing.