Now I'm confused again. Dengeki's article seems to say that the city in Persona 5 is reminiscent of Tokyo. Does that mean that it isn't actually Tokyo after all? or it it just the translation?
http://dengekionline.com/elem/000/001/004/1004572/
And it says something about the contents of the Persona magazine too.
The Japanese wording in previews like that have essentially referred to Tokyo in somewhat of a comparative abstraction. "The game takes place in The Big City this time, resembling places not unlike our own Tokyo." (That's paraphrasing, mind, and not an actual translation.) They make it sound like it's evocative, but not necessarily an outright 1:1 copy, either.
On the other hand, I recall at least Dengeki's print preview (though probably Famitsu's, too, as Atlus has a history of giving them the same marketing copy) having wording that more explicitly implied it was Tokyo proper the game depicts. (上京する, for reference to any of the other Japanese speakers here. My dictionaries tell me that word doesn't have to specifically refer to Tokyo, but I've almost never seen it used for anything else, at least for stories taking place in contemporary times.) But most of the time it's also proactively cagey, so it's hard to be 100% certain.
Personally, I'm in the camp that it is Tokyo Tokyo unless proven otherwise. There's too much of what I've seen of that game's footage that reminds me of where I personally used to live when I first stayed there for it to not be, barring some weird lore about reality stuff or something.
Maybe they don't want to out and out divulge it yet because Tokyo proper has traditionally been the domain of mainline Shin Megami Tensei games? Hard to say.