Hi there. 👋

While I'm not exactly sure on how Intercom triggers these emails, you can change how the email functionality works by toggling Allow conversations to continue over email. This option is found in your Setting > Security > Security Settings

With this setting disabled:

• If the conversation was started in the Messenger on web, the email notification will link to the webpage with the messenger installed. 
• If the recipient has never visited a webpage (on your site, or in your web app) with the Messenger installed, no email notification is sent. For example, if a user has only interacted with you in your mobile app.
• In these cases, we recommend that you enable Intercom push notifications in your app.
• Group conversations are not supported with content in notifications disabled, so your customers cannot add people to conversations by CCing them in an email, and your team cannot add additional participants in the Inbox.