I can't understand what you mean. Even though the configuration file is replaced with an external one, it is still found by the Server in the original folder, hence the relative paths included should not change.

If you want to use environment variables to modify the contents of the configuration file, this is possible, provided that you prepare the file, by placing references to environment variables in the settings that you want to determine from outside.
References to environment variables have the form $env.xxxx, where the "env." prefix should also be enabled by adding the
<env_prefix>env.</env_prefix>
setting.
So, for instance, you can write
<logback_properties>$env.LOG_CONF</logback_properties>
to have the path of the log configuration file searched in the LOG_CONF environment variable.
Note that this can only be used for the whole setting value, not for a part.