For me, I engine brake to a stop with all my manual cars or manual motorcycles. I just prefer engine braking.
Never had a transmission issue/problem engine braking with all the cars and motorcycles we have owned be they cheap (our Hyundai) or expensive (our Porsche).
I also coast (neutral) everywhere I can (when it's safe to do so).
Really, it's do what you like (or what's natural), it's your car/motorcycle.
YMMV.