Right, I can see where this went wrong. Flixbus operate long distance, often international, services and I was surprised that you said they were taking bookings for a short journey like this. But having tried it is obvious that they are only doing it if the seat is already booked later on, it's a way of making a little extra profit from the seat. And they stop about 1 hours walk from where you need to be. This isn't really regional public transport, there is no guarantee you could use it on any given day (like a flight).
The real regional buses and all the trains you need would be covered by the BayernTicket day pass, €25 for first person,€6 each for up to 4 more. On a weekday travel after 09:00. Buy one ticket for the number of people (up to 5) and write names as on passports in the blank boxes. Check train and bus schedules at
https://www.bahn.com/en/view/index.shtml
click the box "Local transport only"
clever tip, trains towards Fuessen leave Munich Hauptbahnhof (main station) a few minutes before each hour and Munich Pasing station on the hour. By boarding at Pasing at 09:00 the Bayern Ticket is valid nearly an hour earlier than from the Hauptbanhof! If it's more convenient you can buy the BayernTicket plus short trip tickets to Pasing at Hauptbahnhof and travel at 08:53
The stop name for Linderhof is "Linderhof Schloß, Ettal" - there are some with similar names in the database which are far away.