Multiple HTTPS sites with multiple Certificates under the same Virtual Server

I do not see any conflict / issue with such configuration if the LTM policy or iRules & SSL configuration is done properly. Now As vServer is configured using iApp template, you will need to modify changes restrictions on the iApp template in order to make changes on the vServer.

But you will also need to consider other side story. As both ADFS & the new URL will be on common vServer, whatever changes you will make on the VS, all the changes will be applicable to both applications. Personally I would prefer to have dedicated vServer for services like ADFS. Otherwise having normal URLs on the common vServer works fine.

Hope it helps!