The thing is it’s not really a manual mode, it’s not an after thought either as all auto Toyotas and in fact most auto cars in general from the 90’s use that lay out.
It’s not really meant for changing gear manually, it’s actually meant for engine braking when going down hills etc. Obviously you can use it to change manually, however you need to be good at judging when you need to select the next gear or you will hit the limiter for a good few seconds before the change.
I drive a manual BTW, clutches and manuals are best.
EDIT: It seems they are meant for changing manually, in which case I agree it's an afterthought as that layout has been the same for a long time.