No, this setting is stored in the database, so this will be inherited. If the instance is for testing it does makes sense disabling this by uncommenting:
DISABLE_NOTIFICATIONS=" -Datlassian.mail.senddisabled=true -Datlassian.mail.fetchdisabled=true -Datlassian.mail.popdisabled=true"
Otherwise you will have 2 instances sending notifications on the same issues.
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