This question comes up for me as in a very large organization with hundreds of projects and teams, the Jira admin over time have introduced custom fields and types that don't or didn't exist in Jira and now they do are will likely do in a future release.
For instance types like Theme and Initiative don't exist as native type in Jira version 7.13. We have created custom types for this as we have created custom field for Team.
However, I know Jira Portfolio has both of these as native type and field.
[Q] How does Jira resolve name space conflict between native types & fields to custom types & fields?
I imagine conflict being resolved when one views project & issues in Jira Portfolio.
This conflict could appear from Jira Portfolio if one is creating Theme of Initiative there and propagating changes into the Jira project.
Has anyone encountered similar issue?
It is a matter of future proofing use and behavior in relation to the product evolving as like all product do.