3CX can only work off of one NIC/IP.
When provisioning, it will include the IP as you set in the 3CX system. The SIP packet will always go to the server in order to set up the call. You need to look at the packet to see how the call is being set and what the SDP is doing.
I would do this for the current set-up and then take two phones (for the extension to extension testing) and put in the same LAN/VLAN as the server and test again. Hopefully, this will show the differences.