They could be, but if you’re then referencing routes.js and useraccounts-configuration.js in the same directory like your example shows, that means they’re in /client (outside of the imports directory), and will be eagerly loaded. If you wanted to update /client/main.js with something like:
import '/imports/startup/client/useraccounts-configuration.js';
import '/imports/startup/client/routes.js';
then no problem at all. Or any directory within imports really, like:
import '/imports/config/useraccounts-configuration.js';
import '/imports/config/routes.js';
The Guide/todos app are just suggesting a structure, and recommend keeping the contents of the default eagerly loaded files (like /client/main.js and /server/main.js) to a minimum, to help better control load order.