Hi,
Windows installer installation shall work if considered listed points mentioned in below link.
https://learn.microsoft.com/en-us/windows/win32/msi/using-windows-installer-with-a-terminal-server
What make this case special is that the skype for business web plug-in might have additional requests when deploying on a remote server which you could consult the experts in Office 365 or Skype for business.
https://learn.microsoft.com/en-us/answers/topics/office-skype-business-server-deployment.html
Though I am not familiar with Skype for business, I still would like to share some reference links that might be helpful for you:
https://social.technet.microsoft.com/Forums/lync/en-US/188d327f-9279-4302-9574-71120f57d7cc/deploy-o365-skype-for-business-within-rds-server-farm?forum=sfbfr
https://learn.microsoft.com/en-us/skypeforbusiness/plan-your-deployment/clients-and-devices/vdi-environments?redirectedfrom=MSDN
https://support.microsoft.com/en-us/office/trouble-installing-the-skype-for-business-web-app-plug-in-958fc5f1-2d6f-42e3-815d-a9516c591274
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Hope this helps and please help to accept as Answer if the response is useful.
Thanks,
Jenny