See subject, it seems as though this is not currently possible. As I've read in the thread ...
... the dotCover command line does not work when the TargetExecutable is vstest.console.exe and one of the TargetArguments is /InIsolation. It seems both are required to test appx containers from the command line.
Is there any other way to automate the generation of a HTML coverage report for appx test containers?