Best Practices, To each its own.
For Pre-stage / initial deployment I deploy the package for zero touch provisioning to really lay it down / guarantee it's on the machine AT enrollment.
However, I also utilize the Settings -> Jamf Applications -> Jamf Connect Payload to configure the Minor & Maintenance auto-updates for everyone in scope of the Configuration Profile.
This has only bitten me in the butt once & was a relatively easy fix. (During the 2.9.0 release, Jamf Connect had a bug where it populated prematurely during ADE at the Apple Setup Utility Window) but besides that, I think auto-configuring updates as long as you're on top of management is a great way to go.