Geographical data: I am in NYC, reside in Queens, work in Manhattan, and visit all 5 boros and nearby suburbs all the time. In other words, pretty much at the center of the civilized world, so anything I am unaware of is completely unimportant 
Most of my fast food joint visits are emergency food stops on road trips, almost never as a planned meal, so even though I know of some of the top 25 (and maybe even know of a location near me) doesn’t mean I’ve ever hit them.
I see and hear ads for Sonic (#13) all the time but cannot recall ever seeing one. I visited their website and apparently they are drive-in only, and there is no space for drive-in restaurants in NYC! I found their online locator and there is only one within 30 miles of me, on a local route (Rte 17) in NJ that I do travel on a few times a year, but not on the stretch that I go on.
I have been to Arby’s (#14) and recall thinking their roast beef sandwiches were better than those at Roy Rogers, but it’s been 25 years since I’ve been in one. There are not many around. There is one not too far from me that I pass by from time to time, but other than that they’re pretty rare, so I’d have to intentionally set out to eat there.
There used to be a Jack In The Box (#15) near me that I passed by on a bus every day on the way to school. There was never more than 1 or 2 people in it, and my friend and I used to make fun of that fact as we went by. I never went there myself before it closed about 15 years ago, shortly after they took a hit in the news from some kind of E. Coli outbreak traced to their chain. Thus ends my awareness of JitB; I have not seen or heard commercials for them that registered with me. I didn’t know it was a national chain that still existed.
I am pretty sure I’ve had Domino’s Pizza (#9) but not by my own volition for 30+ years, and I wouldn’t call them a “chain restaurant” as nobody visits one and sits down to eat there, they’re delivery only AFAIK, right?
Rounding out the Top 25, I have never been to a Dairy Queen (#21) or a Denny’s (#24), though I have seen them while driving around the Northeast somewhere. There doesn’t appear to be a DQ in NYC or Long Island, though there are quite a few in Northern NJ. There are only 2 Denny’s found near me, both in parts of NJ I don’t often visit other than by passing through on the NJ Turnpike (near Rahway and in East Brunswick).
I know I’ve seen Panera Bread but mostly in the ring of suburbs around Baltimore, where I lived for 2 years or so. There’s apparently one very close to me that I must have noticed at least subconsciously, but have never visited.