@bhayes the GDPR changes cover all aspects of the Atlassian products. The changes are related to the Jira API, and are not specific to apps. The reason this group is specifically targeted in the communications is probably because the bulk of Atlassian customers depend on one or more apps that are available on the Atlassian Marketplace and as such any breaking changes that are not mitigated by these vendors will have a large impact on the shared customer base.
However, the Apps that are developed by vendors use the same API’s that you are probably using, hence these changes will also effect your program.
If you are an admin for a company, your will probably still be able to get most of the information that you are seeking as your company will get more control over the data for employees compared to access to individual users.
If you need to access PII of individual users that are outside of the domain of your company, you might want to consider implementing 3LO, which will allow you to get their explicit consent.