In episode four, Varys is picking up what Sansa has indirectly put down and he's following the breadcrumbs she's laid out for him. It's obvious that Varys was already second guessing his Queen's choices; we see as much during season seven after she executes the Tarly men by dragonfire. Now, he's realising that there are other options and he's not afraid to handle the situation like he's done before.
While I admire Varys confronting Tyrion about the concerns they both share and bringing up said worries to Daenerys when she reveals her plans to burn down King's Landing, I'm worried about how brazen he's being. It's one thing to talk in riddles and sly remarks that convey a tease of what you might be plotting, but it's another thing to straight up tell someone, "Hey, I'm plotting treason." Considering how hard Tyrion is clinging to his loyalty for Daenerys, it seems clumsy for Varys to play his cards so openly, no matter how friendly the two are. Here's hoping his honesty with Tyrion doesn't result in his untimely end.