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Associating project fields to custom fields has a lot of advantages. Simply, powerful, just like with any other custom field.
Here are some examples:
Review your project fields in almost all JIRA screens
You can see your project field when it is associated to a custom field in almost all JIRA screens.
JIRA does not provide us, on the creation issue screen, the project on which the issue is going to be created. For that, project fields could not be reviewed on issue creation screen.
Search in the issue navigator by a project field
It is possible to search in the issue navigator for your project field when it has a custom field associated.
View project field value in a column on issue navigator
It is possible to view in the issue navigator columns of your project fields when they are associated to custom fields.
Work with project fields in any gadget, not only in Profields ones
It is possible to configure gadgets that work with custom fields with project fields now.
View at issue screens
It is possible to view project fields values at issue screens.