It's pretty obvious the two are separate continuities, given how often Super presents ideas that clash or outright go against GT's continuity. Shin and Kibito split in Super yet stay as Kibitoshin in GT when there'd be equally zero need to, Dragon Balls are used leisurely with no hint of them gathering Minus Energy, etc. As such, whilst you could argue Beerus and Whis exist and simply didn't interact with the main cast for one reason or another (Beerus not having the SSG dream and sleeping far longer), there's no real evidence for it. The only thing hinting at them existing in the same timeline is special dialogue between SS4 Goku/Gogeta and Beerus in Xenoverse, but that can be took as a grain of salt when the whole game's about cross-dimensional shenanigans.
It's also worth noting that, whilst Toriyama's input isn't as large for Super as what many believe, he did still create the two characters as well as the main plot of BoG. He also created DBO which completely goes against GT's continuity and even referred to it as a "fun side story" making it apparent how divorced from the sequels featuring more input from Toriyama GT is.