GT and Super are definitely different timelines. No one goes SSJB, mentions Beerus and Whis or does/mentions anything else related to Super, because Super didn't exist when GT was made. Until Toriyama flat-out says that GT is in the same world as Super, they're separate.
Second, even if they were in the same world, Zeno is like Beerus, but even more fickle and insane. I can maybe see Goku contacting him to help with Omega Shenron, but Zeno's "solutions" are worse than anything Baby or Super 17 were trying to do. Zeno is not a good guy, and neither is Beerus. They both destroy planets and even universes without batting an eye.
Finally, I disagree with the idea that Zeno is untouchable. No matter how much hate it's getting, Super is still successful. I doubt they'd end it after just one more arc, unless this arc is very long. With that in mind, if I told you at the beginning of Z that Goku would be able to destroy a planet with his finger in less than 100 episodes, you'd have thought I was crazy, but it happened. The same thing's true here. A surprising amount of people think Zeno can't be surpassed, but I say give it another hundred episodes and who knows what could happen? Zeno's power is enormous, but I doubt it's limitless. It would kinda go against the whole "Goku can surpass anyone" thing if he was.