If I use Ho-Oh GX's "Eternal Flame GX" attack, can I place a Stage 2 Pokemon like Charizard GX from my discard pile directly onto my Bench?
Yes. The attack does not specify that the selected Pokemon have to be Basic Pokemon.
Source: Burning Shadows FAQ (2017-07-20), TPCi Rules Team (2017-08-03)

Relevant cards

Note: All applicable cards may not be listed below.
SM3_131
SM3_21
SMA_SV50
SMA_SV50