You can install multiple SSL certificates to IIS or apache, as you may be hosting multiple sites of which each one needs it's own SSL. Both IIS and Apache have supported this for a long time.
Where filemaker gets involved though it gets complicated a bit. FileMaker *wants* to be the web host for all of your port 80 traffic inbound to the server. It installs it's own rules for IIS and apache on installation. There may be some customization work on your end to flip back and support multiple sites again, and subsequently support multiple SSLs.
Since my recommendation is to not use a filemaker server as a dual-use server with a web server (like XAMPP or IIS/ASP), my ultimate question would be why would you need multiple SSLs?
We are running a MacMini dedicated to FMS 14 only as a one machine setup, serving FMP and WebDirect. One of our customers ask us to deploy their SSL Certificate (port 443) for their WebDirect solution. We are not sure, if we use their SSL Certificate, how will it effect the other customers access to the same server.
Is a SSL Certificate valid for all FM files on this server? Or can the SSL Certificate just be valid for a certain admin group?
Without having sufficient SSL Certificate knowledge or experience, I rather tend to recommend a dedicated FM Server with a SSL Certificate. Would this be the best practise?
The SSL certificate would apply and cover your entire filemaker server. It is valid for the filemaker host and not applied on a per-file basis. So it would work on all of your sites.
If you're hosting for multiple clients and this client is important, you should offer to purchase your own SSL certificate so you can manage it, rather than relying on your client's generosity to cover the other clients you are hosting.
There's also a compatibility issue, as some SSL certificates are NOT compatible with filemaker.
+1 to Mike B's comments. I'd also be curious to know why the client wants to control the certificate.