You of course can, but upon what stimulus do you want to do that transfer, i.e. how do you want to trigger the DMA?
If you base it on CH1 or CH2, which are the encoder inputs, you'll get 1, 2, 3, 4... or 4, 3, 2, 1... when you turn/move the encoder, which I doubt is what you want.
Maybe you should tell us, what is your ultimate goal.
The timer in encoder mode runs automatically, with no involvement from the processor. You don't need DMA, you read it out only when you want to know its current position.