Summary

It is possible to restrict custom fields' context, making them available only to specific projects.

But, as a consequence, those fields will not be displayed as options during the field mapping step in the CSV import (external system import) process unless you are importing issues into a single project that is applied to the available context(s).

Given that the import functionality can be used for larger administrative tasks, such as importing a big number of issues into several projects at the same time, it might require a lot of manual work in case you need to change a big number of fields' contexts so they can be mapped during the import process.

Suggestion

Make it possible to map fields with restricted context during the CSV import, and have Jira handle properly if the field is not applicable for a certain project, preventing any values from being created during the import in the issues of those projects, but preserving the ones that can receive such values.