It is possible to send download links in your standard Shopify order confirmation emails. The downside to this is that the link will be sent for every order and not restricted to the orders that have files.
To do this.
1. Disable Sky Pilot emails
Uncheck "Notify customer of downloads for new orders via email"
Click Save
2. Add download link to Shopify order confirmation
In your Shopify settings edit Your Order Confirmation Email Template
Add the following snippet to your order confirmation template
<a href='http://{{shop.domain}}/apps/downloads/orders/view/{{email}}/{{id}}' class='btn'>
Download My Purchases
</a>