In my opinion it is unlikely that Fandaniel would have the means to dispose of Zenos on his own. Zenos is more a means to an end for him, if he even is a grand schemer. To me, it seems like his motivations are largely base, and that this is one reason he was probably easy to ferret out and raise into his Convocation chair. The allure of getting wealth and gold and whatever else while being largely untouchable by most people.
Given his surprise at the fact that the last Unsundered is no longer around, it could be that he aligned himself with Zenos originally in order to have a lynchpin to bully the Unsundered with, given how powerful Zenos has become. He seems to be antithetical to the Unsundered. He's sundered first of all, secondly he's the first Ascian we've been shown that wore distinctly different robes from the normal Ascian robes. I imagine he resents the idea that he's tempered by Zodiark without having even known it, before being raised to his seat.
To me these things say that rather than looking to backstab Zenos or off load him first chance he gets, that Zenos is a long-con key item for him. I believe he wishes for Zenos to take over Zodiark and then use whatever it is that Emet-selch implanted in Zenos to control him, thereby effectively controlling the god.
Surely it's longshot speculation, but I'm running with the idea that Fandaniel is heavily inspired by Kefka. Kefka's mind snapped after his magitek augmentation, and now knowing all of the legends to be true about the world he lived in, he resolved to reawaken the Warring Triad. Earlier on we find out that he's become a psychopath who we know relishes in the deaths of hundreds of people at once, "Nothing beats the symphony of hundreds screaming in unison! Uwee-hee-hee!" We've been shown that Fandaniel's mind snapped once with the zodiac stones, and it's quite possible that his mind snapped again after being re-raised to his old station, for as of now, we know not which shards were chosen to scour for individuals to raise up. I think the most concrete parallel between Fandango and Zenos is that they both have their humanity on the back burner. Though rather than being in love with death and destruction, Fandango is in love with manipulation.
There won't be any reason for Fandango to kill Zenos or vice versa if the manipulation that Fandango seeks to enact on Zenos plays into Zenos's wishes. Personally I don't think either of them will die before 6.0. I think an interesting happenstance may occur wherein the other Sundered Ascians either ally or oppose Fandango, and Fandango has Zenos start putting down the other red masks.
We might even get an Ascian on our doorstep, begging for intercession and sanctuary. If not in earnest, then perhaps in ruse.