Yes. When you create the editor on the page, you can override
CKEDITOR.replace(editorName, {
height: 448,
width: 448,
customConfig: '/path/to/yourconfig.js'
});
In fact as a performance recommendation you can put all the configuration options here and save the loading of the config file separately. You might do this in a shared JavaScript file of your own, parametrized to override specific values for a page.
UPDATE in response to comment
A separate config file can be used like any other setting (look above with customConfig. If you don't want any custom configs loaded use
customConfig: ''