If I remember correctly, Gemini works by pushing whatever events you enter in Gemini through to the stock calendar app, as well as reading the stock app to show events on screen. Presumably, for it to work on different phones there must be an API which Gemini is calling to add or change an event in the stock calendar, which is consistent on every phone. Further presumably (doing alot of presuming here, I know), part of that API is something to set the alert type (otherwise the stock calendar might not be giving any alerts at all for events entered in Gemini).
So, feature request for Gemini: an option to disable the setting of alerts in the stock app for events entered using Gemini.
This wouldn't prevent existing events entered directly in the stock app from being double-alerted, so the same feature request could do the opposite as well, i.e. disable the alert in Gemini for any event which was entered or changed using the stock app. Whether Gemini works that way (i.e. if it can tell whether a change in a stock calendar event was due to Gemini requesting such a change) is another matter. If it doesn't, it could perhaps set the event type in the stock calendar for any event which gives it an update, but I don't know if the alert type can be set independently that way.