There are a lot of options now, that's very true.
It is true that you need different endpoints for the .NET and SL data portal hosts on the server. You can put them in different virtual roots (web projects) or not as you choose - either way works from a technical perspective.
It is not true that they need different ports. They are just different endpoint names (like different web pages) and can co-exist in the same virtual root, under the same port, with no problem. In this case you'd just have two svc files and two service endpoints in your web.config.
The real issue for most people, I think, is that the SL data portal host has to be available to the SL clients, which may mean it is on a public web server. It is quite possible that your .NET users are internal, and so would probably access a data portal host inside your firewall. That seems like the most likely reason you'd have two app servers.
And even then you don't necessarily need two app servers. The SL data portal host machine can act as a "relay", simply routing all calls to the real app server.
This blog post should be helpful
http://www.lhotka.net/weblog/CSLALightDataPortalOptions.aspx
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