In other words, do abilities that decrease the encounter rate state with the decreased encounter rate of Stealth O-Power, or any other effect that limits but doesn't completely stop encounters with wild Pokemon?
Yes,they do stack because they are not one of the same thing but two different things that reduce the encounter rate of wild Pokemon.It's like using Hatching O power and having a Flame Body/Magma Armor Pokemon.
List of abilities that reduce encounter rate.
Hope I helped!