The --override flag in otelcol-config was added to allow overriding configuration when using conf.d-available files. Configuration is loaded in lexicographical order. The overrides file starts with 99- and none of the files in conf.d-available start with a number. The result of this is that the configuration cannot be overridden as expected.
We should add a prefix of 10- to all files in conf.d-available. We will need to determine how to migrate the symlinks from old installations as the symlinks will no longer be valid after this upgrade.