To publish such an app, just configure the app like you would when you publish the whole server. Then connect to Azure AD by PowerShell, you have to authenticate with global admin permissions:
Import-module AzureAD Connect-AzureAD
Or if you haven’t installed the AzureAD module, then just use:
Install-module AzureAD Connect-AzureAD
Then we have to select the app you just created. To make this easier, I added an Out-Gridview to let you choose the correct one with a UI:
$app = Get-AzureADApplication | Out-GridView -PassThru
Now you can validate if you have selected the correct application with entering:
$app | fl *
The last task is now to change the Homepage of the App. This property is available in the Webinterface, but Readonly:
But we can change this with the following PowerShell command:
Set-AzureADApplication -ObjectId ($app.ObjectId) -Homepage "https://webserver.contoso.com/Special/StartPage.html"
I hope this will help you in one of your projects.