Found it ! Replace the NotificationMailer class with some composer.json magic, in the root folder. Your src/Flarum/Notification folder must contain a class with matching filename, name & namespace.
"autoload": {
"psr-4": {
"Flarum\\Notification\\": "vendor/your/extension/src/Flarum/Notification"
},
"exclude-from-classmap": ["vendor/flarum/core/src/Notification/NotificationMailer.php"]
},
In the send method, you can then call the replyTo method on the Illuminate\Mail\Message object.
