How do you properly configure a logger in application like that?

Just imagine a callsite that configured a logger in another way, and then imports the utils module for a single function: its configuration getting overridden by the one in utils.

There are plenty of ways to structure code so this does not happen, but simply "do not do anything at the top module level" will ensure you don't hit these issues.

Usually you would do it in your main function, or a code path starting from there. Executing code with non-local side effects during import is generally frowned upon. Maybe it's fine for a project-local module that won't be shared, but it's a bad habit and can make it had to track down.