Firstly, the main problem here is that the end result is unexpected and non-intuitive to users.

1. Create a new project
2. Create a new issue type
3. Add a custom field that only applies to just that issue type
4. Create a few issues in the new project with values in the new custom field
5. Add the custom field to your Issue Navigator as a new column

When you create a query for the project, the new column is not displayed unless you also select the new issue type as part of the filter. Selecting "Any" doesn't help either.

So we have a case where all the issues in the new project are allowed to have the new custom field, but it still won't be displayed in the results. Most unexpected.