You can easily deploy MSIX applications via Intune to managed company devices. I will describe the required steps in this article.

 There are 4 steps:

  1. Export the certificate to a .cer file file from a computer where the certificate has been installed.
  2. Create the application in Intune:
    1. Create the application group
    2. Import the MSIX file
    3. Assign to the group
  3. Test on the client
  4. Monitor the deployment

Export the certificate to a .cer file from a computer where the certificate has been installed

Description Picture
Start certmgr and select the certificate you want to export.
Export as a DER certificate.

Create the application in Intune

Description Picture
In Intune, go to Client apps -> Windows enterprise certificate.
Browse to the certificate (cer file) you have created earlier. Upload the file.
The result.
Go to Groups and click on [New group].
Fill in the group details as per example.
The end result.
Go to Client apps and click on [Apps].
Click [Add]
Select 'Line-of-business app.
Browse to and select the .msix file.
Select an icon for the application.
I used 7ZIP to open the .msix file and extract the icon file from the 'Assets' folder.
Click [Ok] when done.
Click [Add].
See the progress bar to check the import.
After waiting a while you can add groups to the new application.
Click [Assignments].
Click [Add group].
Select [Available for enrolled devices] from the pulldown menu.
Click on [Included groups].
Click [Select groups to include].
Select the gruoup you have created earlier:
And click [Select].
Click [Ok]
Click [Ok]
Click [Save]

Test on the client

Description Picture
In the company portal select 'Paint.Net'.
Click [Install]
You can monitor the progress.
And the end result: a working application.

 Monitor the deployment

Description Picture
You can check the installation status in Intune.