The Bayern-Ticket would include all of your transportation, from anywhere in the 'M' (downtown) zone in Munich after 9:00 on a workday, by bus, S/U-Bahn, or tram to the Munich Hbf, from the Hbf by regional train to the Füssen Bhf, and the bus from Füssen Bhf to near the ticket kiosk in Hohenschwangau, plus from there back to your starting point in Munich.
However, you mentioned possibly wanting to go earlier than 9:25 (Arr. Hohenschwangau at 12:20). But to take the 8:40 (arr. Hohenschwangau at 11:20) , you could not start using the Bayern-Ticket before 9 AM. Full fare for the trip using the earlier 8:40 RB is 29,10€ (for 1), and that 1) does not cover transportation to get to the Hbf in Munich or the nominal bus fare from Füssen Bhf to the castles, and 2) is only to Füssen. You would still have to buy the return trip ticket, which could be a Bayern-Ticket anyway, to get back to Munich.
But the RB that leaves the Hbf at 8:40 gets to Geltendorf at 9:07; from there on you could use the Bayern-Ticket the rest of the day. An MVV single trip ticket to Geltendorf from anywhere in the 'M' area is 10,50€/P, and you can use the MVV ticket at any tine. So, you could buy a Bayern-Ticket and an MVV ticket to Geltendorf and get on the 8:40 RB. When you got to Geltendorf at 9:07, you could start using the Bayern-Ticket, and you would get to Füssen Bhf (not the ticket kiosk) at 10:41, or the bus stop below the ticket kiosk at 11:20.