Hi,
I am also having this issue, specifically using Nessus scanner, we're seeing many vulnerabilities showing for Microsoft3DViewer, 3D Paint, Web Media Extensions Library RCE, WebP Image Extension RCE, MPEG-2 Video Extension RCE.
I have found that to get all users that have it installed, Get-AppxPackage -Name package name -AllUsers.
This will show the application, current version, and under PackageUserInformation, what users have that version installed. These will be listed by version so you may have more than 1 listed. If the user has been deleted from the machine, it may only show the SID for that user. The easiest way to pin this back to a username was by checking HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\ProfileList. Depending on how the user was deleted then you may not even have a record here. We found that some old user accounts were deleted from a device by just deleting the user folder in C:\Users.
Something else I have found is when deleting users from a device showing these vulnerabilities, if you delete the user via Control Panel > User Accounts > Configure advanced user profile properties, this will complete a more in-depth deletion of the user and has helped with clearing old user records on these applications.
Although it doesn't appear to resolve everything for all Appx Packages, I have had success with the following command, Get-AppxPackage -Name package name | Remove-AppxPackage -AllUsers
Previously I had tried all different ways, even attempting to rebuild the database library where this information is stored. However, this resulted in a large number of user profile issues and I wouldn't recommend it.
On a larger scale, there may be something you can do within Powershell and a logon script, however, I've not reached that stage yet. If you find a way with the help of this information, please share.