A Webex bot conversation must preserve conversation context between incoming messages. If each incoming message starts the Webex Connect flow from the beginning, the flow is treating every webhook event as a new start event instead of waiting for the next message from the same user. The Receive node is the correct mechanism for continuing the flow after the initial webhook trigger. It should use a custom event that matches the user email, because the user identity is what links the next inbound message to the same conversation path. Matching the bot email would identify the bot endpoint, not the specific human conversation participant.
Creating multiple webhooks for different steps would fragment the design and still would not preserve state cleanly. A Call Flow node is useful for modularizing logic but does not by itself wait for and correlate the user's next message. The Receive node with the user-email custom event keeps the conversation from restarting. Reference: Webex Connect Help, Receive Node and flow debugging; Webex Connect Webex Chat
/Webex Engage documentation.