I have not been able to get that to work (yet). I know that SSMS has been problematic in the past with App-V due to it having COM+ components. I did not investigate if it still has Com+ but suspect that was the cause and that MSIX does not support it either.
Did you find a solution? I tried packaging this but ssms does not work. SQL Profile etc works though. I tried running process monitor but couldn't work out what was wrong. If I install SSMS from setup and then install SSMS from the MSIX package on top it works.