I don’t see why not, the only problem I would see is when running your 36V, you’ll have the possibility of have one fully charged battery in series with two lesser charged batteries…
Just tap off the first two batteries for the 24V and the first and last for the 36V.
Sure should be able to be done. I have a 16 1/2ft with a 109#-36V on the Bow and a 55#-12V on the Transom. Chews through the juice running both at the same time, but getting 6mph and putting out a low Wake
I can go almost anyplace on the water I want, thru the thickest slop to reach Bass in hidden backwater bays.
Your battery capacity for the 36V will be limited by how much capacity you pull out via the 24V motor first, or in conjunction, but you certainly can tap you battery string in this manner.