I installed the 4GB patch after the MCP, and have since upgrade MCP without any issues; I don't think they're incompatible in anyway... does installing one overwrite the other?
From what I've understood, whenever you apply the MCP it restores a backup of the original Morrowind.exe first, so if you'd apply MCP last then it would probably overwrite anything else done to the .exe before. But the exe optimizer and 4 GB patch don't, so they
should work if installed after the MCP.