According to the WWDC2020 session "What's new in Universal Links" (10098), the "apple-app-site-association" file will be served and retrieved by an Apple's CDN instead of directly retrieved from the client.
If the App has associated domains that are not publicly accessible, because they are for example only accessible using a VPN, it seems that there are only two options: using "Developer mode" or "Managed mode".
If the App has associated domains that are not publicly accessible, because they are for example only accessible using a VPN, it seems that there are only two options: using "Developer mode" or "Managed mode".
Developer mode only works with apps that are signed with a developer profile.
Managed mode requires consent from the MDM admin.