CORMANT, Firstly, apologies for the delayed response.
Based on my understanding of your issue description, you are encountering SSL related problems with your clients using Android 9 below. I understand that you have already imported Certificate R6 to each mobile device as a workaround. However, you are looking for a proper/alternative way to install CA Certificates for Azure App Service. Is that correct?
Regarding your concern about the Intermediate CA1, Intermediate CA2 & Root CA included in the pfx file not being detected by online SSL Checker tools, it is possible that the SSL Checker tools are not able to recognize the certificate chain. This can happen if the SSL Checker tools do not have access to the complete certificate chain.
If your certificate authority gives you multiple certificates in the certificate chain, you have to merge the certificates following the same order ( if you haven't done this already so). For more information, please checkout this doc section : Merge intermediate certificates
- Refer: Doc for more details Troubleshoot domain and TLS/SSL certificate problems in Azure App Service about the issue.
- Ensure the prerequisite are met (doc -Add and manage TLS/SSL certificates in Azure App Service)
- App Service has a list of Trusted Root Certificates which you cannot modify in the multi-tenant variant version of App Service - Root CA on App Service
Kindly let us know, happy to follow-up with you further.
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