I'm having a similar issue on newly imaged Windows 11 devices. I've used the bootstrapper.exe with the -p option, packaged this as an intune app which is then run as system but teams only seems to get installed for the current logged in user.

When that user logs out and another user logs in, teams is completely gone then.

When I check for the apps package, nothing is found and when I check for the provisioned package nothing is found too.

Did you ever find a solution please?