None of the standard SCCM application detection methods work for APPX packages. For an APPX package use "Use a custom script to detect the presence of this deployment type" and this command line as the script (modify for the package name and version number that you need obviously):
if ([version]((Get-AppxPackage *AppUp.ThunderboltControlCenter*).Version) -ge ([version]("1.41.648.5"))) { write-output $true }
Enjoy!
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