I'm looking to book a oneworld Classic Flight Rewards itinerary that includes 2 transits (<24 hrs) and 1 stopover (>24 hrs) in Tokyo.

Would this be allowed? or does the stopover count as a transfer as well?

According to Qantas:

14.5.4 The following Stopover conditions apply to oneworld Classic Flight Rewards:

(a) up to five free Stopovers are permitted;
(b) additional Stopovers are not permitted;
(c) only one Stopover is permitted in any one city in the Itinerary; and
(d) only two Transfers may be taken at any one city in the Itinerary.