For those managing Apple Software Updates with Munki, Jamf Policies or other scripted/binary/agent methods powered by the `SoftwareUpdate` binary, take note of this post from the team behind Munki:
TLDR: we should be using MDM commands on DEP enrolled machines and/or managing Apple software updates exclusively with configuration profiles, directing all updates through the native macOS process in System Preferences.
Here is a Jamf Perspective, but missing the above detail on software update binary issues:
The reality is that any management system/script/etc that has historically used the softwareupdate binary is not a viable way of running updates moving forward (unless Apple change their trajectory, which I highly doubt).
If your org does not currently manage how System Preferences handles Apple Updates, start. If you are not currently using Automated Device Enrollment (DEP) or an MDM that can push Software Update commands over MDM framework, change.
Start managing your macOS System updates like iOS 😉
Update 2020-06-28: here is a more specific explanation of why the command line installer tools have become unreliable and a possible workflow for Jamf Pro (or similar tools) when you want to manage updates at specific intervals: