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And it is possible to disable FindDuplicates on all projects except selected ones:

Search within Project Configuration ^{(FD v2.3.0 and above)}

It is possible to configure Find Duplicates to always search for duplicates within the currently selected project only.

To access Configuration page follow the steps:

1. Go to JIRA Administration > Add-ons > Manage add-ons > FindDuplicates
2. Press Configure button
3. Select checkbox "Always search for duplicates within the same project"

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User will not see duplicate issues from other than current project when this option is selected.