Its not so much the stick. It is more the TREE in this case

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The Session Initiation Protocol, or SIP, is a new IETF signaling protocol for establishing real-time calls and conferences over Internet Protocol networks.
Each session may include different types of data such as audio and video although currently most of the SIP extensions address audio communication.
As a traditional text based Internet protocol, it resembles the hypertext transfer protocol (HTTP) and simple mail transfer protocol (SMTP). SIP uses Session Description Protocol (SDP) for media description.
SIP is independent of the packet layer. The protocol is an open standard and is scalable. It has been designed to be a general-purpose protocol. However, extensions to SIP are needed to make the protocol truly functional in terms of interoperability.
Among SIP basic features, the protocol also enables personal mobility by providing the capability to reach a called party at a single, location-independent address.
Relationship Between SIP and H.323
Both SIP and H.323 define mechanisms for call routing, call signaling, capabilities exchange, media control, and supplementary services.
SIP is a new protocol but promises scalability, flexibility and ease of implementation when building complex systems. Over the last couple of years, the Voice over IP community has adopted SIP as its protocol of choice for signalling. SIP is an RFC standard (RFC 3261) from the Internet Engineering Task Force (IETF), the body responsible for administering and developing the mechanisms that comprise the Internet.
H.323 is an established protocol that has been widely used because of its manageability, reliability and interoperability with PSTN.
H.364 is allong the same line butmore focused on Video (30 Fps i believe is possible) .
So you got a good Video Phone, i do not think that 3CX currently supports video phone but i could be wrong.
Now back to your question.
So at what point does the SIP Server care what protocols the two phones talk to each other in...? Have I got complelety the wrong end of the stick as to what SIP is?
Pretty much all the time, the server does not so much care what type of codecs are used. (But i could be completely wrong).