One thing to remember when figuring out which setting, if any, will get a boxed set: they have very thorough data that has shown time and again that about 55% of games are actually homebrew, though only about half of those are strict rejections of existing settings, while the remainder are just "will use whatever fits" looser ones. Coupled with the 35% using some form of the Realms, there's a reason products have been largely Realms-centric: between the FR campaigns and the "steal anything generic" campaigns, over half of the games out there can use Realms material.
That said, it won't be a FR box. They consider it covered by the hardbacks, each one acting as a regional gazetteer as well as an adventure path. And it's the adventure material that really appeals to the DMs whose campaigns are patchwork, not the hyper-detailed setting treatments. Most DMs just don't care about canon like that, nor should they if it's meaningless to their games. What happens at their table is what's important. They'd be just fine if the setting never advanced any further.
Eberron I can see as it's a popular setting and has a broad appeal of being not straight jacketed as a pseudo-medieval-European setting. And there's the fact that it's a fixed setting; when they considered advancing the timeline two years for the 4e version of the setting, the feedback was overwhelmingly negative. Time and again the idea has been rejected. For a perennial product, it's a logical choice.
Greyhawk, according to WOTC's data, is supposedly the second most popular setting, with about 5% of the games (all other setting combined are the remaining 5%). And they seem to have finally approached it as a separate setting. Ghosts of Saltmarsh isexplicitly set in Greyhawk, and there's a sidebar for using it in other settings. So the possibility exists for it to be used, but I kinda think it's going to get the FR treatment in that there might be future hardbacks that are both gazetteers and adventures in one. And like the recent ones, it'll get separate map or accessory packs.
What I found most interesting about that sidebar was not so much that they pushed the Realms into the sidebar, though I can see how that might surprise some based on the track record thus far with 5e, but that the settings listed were the Realms, Eberron, and ... Mystara. Maybe the recent Goodman Games hardcovers are also a way to reintroduce one of the oldest settings to the public.