Make certain scaffold file changes a warning

Problem/Motivation

Follow-up from #3091285: Composer scaffolding fails when permissions on default.settings.yml or default.settings.php is not writable..

Currently all file changes in scaffolding cause an error if they fail. For default.settings.php and similar files, it doesn't matter that much if they're not updated, so we could continue and show a warning instead. We shouldn't do this for all files, but we can do it for some.

Steps to reproduce

Proposed resolution

Remaining tasks

User interface changes

Introduced terminology

API changes

Data model changes

Release notes snippet