Shopify's system doesn't allow users to disable the notification in the setting part. Every activity from customers will be triggered then they will receive an email from Shopify automatically. For example, when an order was created then Shopify will send an email confirmation to them with full details of the order.
Therefore, for those users who are using the Automation Flow with the aim to replace Shopify's default notification then it is impossible to do that. This means, your customers will receive two emails from both Shopify and ManySales.
The consequence of this matter will create confusion for your customer because they receive an email twice with the same content. To avoid this problem, we suggest you visit our article How to avoid overlapping ManySales auto-email with Shopify?
Should you have any further questions, feel free to reach us at email firstname.lastname@example.org for more assistance.