You're looking at it all wrong. CnCNet.exe does contain a list of common executables (I assume C&C95.exe, ra95.dat, sun.exe), but it only uses that to see whether it has to replace thipx32.dll or wsock32.dll, and to auto-detect which exe to start from that game folder.
When the game is launched by cncnet.exe, it gives an extra command line parameter to the game. The dll, being part of the game, can see these command line parameters, and switches the game to cncnet mode when it sees the one it needs (I think the parameter is the server's url).
As for whether the game is C&C95, RA95 or TS, that is of no importance at all. The dll is what the game uses to send all network traffic. Once set to cncnet mode (through the command line parameter), the dll simply sends all traffic from the game to the cncnet server instead of on the local LAN. If instead you start the game normally, it won't be set to cncnet mode, and will simply send the traffic over the LAN.