I know this topic is a few days old, but I've been looking for anyone else who's caught this connection since I think it is right on the money. I'd guess it's something Tyrion will figure out on his trip with Jorah through Valyria or wherever they're headed. It seems to be the best explanation for what Varys will do for the rest of the season. After all, if it isn't the case what is he really supposed to do after Tyrion disappears?

*Does he continue onto Mereen? That doesn't seem likely since he wouldn't have a clear/non-redundant role in Dany's court - and how would he get accepted by her in the first place.

*Does he just give up and head back to Westeros? Doesn't really fit his character, since Daenerys has been his long term goal in the show. And was his show!plan the same brilliant scheme that drunk, despondent book!Jorah came up with? At least Jorah has a better chance of her not killing both of them on the spot.

*As for his potential plans back in Westeros (that is the ADWD epilogue and maybe an appearance in Dorne), I don't think he could have made them had he really intended on going all the way to Mereen. That's a long trip to just turn around and come back. And if he didn't know that he would have an agent in Dany's court (or at least could make that reasonable assumption), why would he start prepping Westeros for her arrival?

So I really think this is the way the show is taking it. And I think it's a strong change since it fixes one of the biggest contrivances (IMO) from the books (that is, Jorah and Tyrion running into each other in the same brothel out of all Volantis, of all the free cities in Essos). Not to say that this is the only explanation - there's the slightest of chances for Aegon to still pop up, and the show has the ability, I think, to gloss over fine details and have the viewers come up with their own explanations. This also assumes Show!Varys's storyline will realign with the books at some point, so there's that.