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Deploying separately from original FastAPI app

You are not limited to serving the MCP on the same FastAPI app from which it was created. You can create an MCP server from one FastAPI app, and mount it to a different app: 
from fastapi import FastAPI
from fastapi_mcp import FastApiMCP

# Your API app
api_app = FastAPI()
# ... define your API endpoints on api_app ...

# A separate app for the MCP server
mcp_app = FastAPI()

# Create MCP server from the API app
mcp = FastApiMCP(api_app)

# Mount the MCP server to the separate app
mcp.mount_http(mcp_app)
Then, you can run both apps separately: 
uvicorn main:api_app --host api-host --port 8001
uvicorn main:mcp_app --host mcp-host --port 8000
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