I believe there are many many more than what you have here. That being said, I've never seen a complete list. I'd be willing to bet money that someone here has a list that is very comprehensive.

You can also go title by title through the NA database like in the example pic I've attached. Note how 10 Yard Fight has both types of box. Not sure if the database is complete though.

I'm not sure what the list is, but it is not a list of boxes with both versions that exist. Most of those are Rev-A only.

I'm not smart enough to figure out what this list actually is, but it's missing most of the black box games, SMB/DH/WCTM doesn't have a box, and Mega Man 4 no rev A? This list is something else.

I got the list from here:
http://nerdlypleasures.blogspot.c...

Does anyone have a list of all REV-A variants?

as per the site you linked to "All the above games have one known, released revision to their ROM(s).  Typically they are referred to as REV. 0 and REV. A or REV. 1. " So sounds more like he was talking about ROM revisions not the rev-a on the boxes themselves.

1942
10-Yard Fight
3-D Battles of World Runner, The
Alpha Mission
Arkanoid
Athena
Athletic World
Balloon Fight
Baseball
Breakthru
BurgerTime
Castlevania
Commando
Deadly Towers
Donkey Kong
Donkey Kong 3
Donkey Kong Jr.
Double Dribble
Duck Hunt
Elevator Action
Excitebike
Ghosts 'n Goblins
Golf
Goonies II, The
Gotcha
Gradius
Gyromite
Hogan's Alley
Ice Climber
Ikari Warriors
Jaws
Karate Champ
Kid Icarus
Kid Niki: Radical Ninja
Kung Fu
Legend of Kage, The
Legend of Zelda, The
Lode Runner
Lunar Pool
Mach Rider
Mario Bros., The Original
Metroid
Mighty Bombjack
Mike Tysons Punch-Out
Ninja Kid
Pinball
Popeye
Pro Wrestling
Rad Racer
Raid on Bungeling Bay
Ring King
Rush'n Attack
Rygar
Section-Z
Sky Kid
Slalom
Solomon's Key
Spelunker
Spy Hunter
Star Force
Star Voyager
Stinger
Super Mario Bros.
Super Pitfall
Tag Team Wrestling
Tennis
Tiger-Heli
Top Gun
Track & Field
Trojan
Urban Champion
Volleyball
Wild Gunman
Winter Games
Wizards & Warriors
Wrecking Crew
Zanac

Not 100% sure on but potentially also DK JR Math, Soccer, gumshoe (Not sure if they have a rev-a box or not)

That should be a good starting point. Its a list of every game with both a 3 and 5-screw version. As a general rule of thumb, the 3-screw carts would be in a Rev-A box (and 5-screw boxes would have no rev-a)