@Wes Reinke, Thanks for posting in Q&A.
For LOB app, if it is deployed via Line-of-business app. then it can't choose the app update time. Here is a link with more details:
https://learn.microsoft.com/en-us/mem/intune/apps/lob-apps-windows
Meanwhile, for the app update behavior, it is controlled by the app itself. Intune can't determine whether it close the application or not when the user is using it. Intune can only help to deploy the app.
To control the app download and install time. you can choose to deploy it via win32 app. In this type, we can configure the start time and deadline time for a Win32 app. At the start time, the Intune management extension will start the app content download and cache it for the required intent. The app will be installed at the deadline time. Here is a link with more details for your reference.
Hope it can help.
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