If I use Tsareena V's "Queen's Orders" attack and discard a Stage 2 Pokemon from my Bench, does it count as three Pokemon including the Basic & Evolution cards underneath that also get discarded?
No, the Basic & Evolution cards are all part of a single Pokemon while in play.
Source: Fusion Strike FAQ; TPCi Rules Team (2021-11-11)

Relevant cards

Note: All applicable cards may not be listed below.
SWSH8_21
SWSH8_21