Maybe. It depends. What do you mean by "custom" - are you talking about the list of users you are sending to, or the actual content of the email? In both cases, how are you making the decision on what to send to whom?
As a workaround, you could set up a rule of "move to this folder" in the assignee's email client, or a "do not actually send it" in your mail server when the sender is JIRA and the email subject matches some expression.
You can define custom messenger - one per user using our addon https://marketplace.atlassian.com/plugins/net.vacom.jirassimo/server/overview
Even further, you can finely tune notifications using JQL and dynamic destinations which can be based on value of custom field in your JIRA issue.
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