We have deployed to the customers https://myapps.microsoft.com portal and this Intune Company Portal not even show apps which are deployed trhu My Apps portal.
Planning and implementing out of the box experience with Windows 10 + Azure EMS + Office 365 scenario. Where end users can buy computers from self-service portal and when device arrives they can set it up without Service Desk or on-site support.
This depends on the situation, and how you would like to enable access to those Apps.
While "My Apps" is based on applications made available through Azure AD, with different sign-in methods, the apps in Company Portal are mainly Apps from the App Store/Google Play or Weblinks that you made available through MS Intune.
Seamless login experience
Federated Company Applications, configured through Azure AD
Access applications configured applications
Apps from App Store/Google Play
Useful web links
Refresh company policies etc.
I marked the main difference in Bold. Hope this helps!
is there an article on those differences? Also, from what I can see, apps in either, are effectively different, and require management of each. Say we setup a LOB app in 'apps' ; its different than that setup in intune apps.