Flow should let bots mark their edit as bot, so it gets hidden by default in watchlist/RC
To match core functionality, the API should also take a 'bot' parameter. For users with the 'bot' right, the edit (for Flow, write action) is marked as bot if and only if they set that parameter. For non-bot users, the parameter is ignored. With this, I guess the main UI would always pass bot: 1.
I guess the simpler version would do it for all actions a user with 'bot' takes, but that's not as similar to core.