And it's not specific to zhonya's interaction with Equinox, happens way too often with Fizz ult as well. I throw it down, so that it attaches as the stasis ends, 90% of the time they are able to flash/dash away. I expect the same thing happens with things like Galio ult as well.
There is a very simple way to legitimase the Zhonya-whatever ability interaction, add "...and stays invonurable for a very short time after stasis ends" to items description.
Actually fixing it would take changing mechanicks of how the game determins if the champion has been affected(not gonna happen). Or some exceptions to how zhonya works, abilities actually affecting the target in stasis but not doing any damage or further cc effects, making them actually not actually untargetable to some abilities, while still apearing so (would have to analise all abilities in lol to implement, again doubt its gonna happen any time soon).