Currently seems like if these two configurations exists, for columns list:
1) user_xxx / All projects
2) All users / project_xxx

Configuration (1) takes precedence.
This may be intended, but giving priority to (2) may have a justification:

If a system-wide column list is defined for a project (different from all-projects defaults), may mean that some specific columns are important, as the administrator judged to include them. These columns may be custom fields that only make sense in those projects.

If a user has defined an all-projects configuration, may mean that the selected configuration is intended as a default for projects where there are not specific, relevant, columns.

So, the user saved "all projects defaults" would replace the system provided "all projects defaults", but not replace the system provided "single project defaults" (unless the user sets a "single project column-list"

I find this use case relevant, when creating project-specific custom fields, or plugin fields.
In this new config behaviour, there is a higher chance that the users will automatically see the new columns, without having to notify users to update their column list customization (even if they never modified that project specifically)