A lot of people call this the true final boss of the game and mainly complain about the targeting seeming to be random. But a lot of people also don't realize that you can use the command menu (slow-mo) and targeting system in this challenge to pinpoint where Yuffie throws her weapon. You also need to recognize that you should use physical damage on orange boxes and magical damage on purple boxes to save a lot of time. I think a lot of people go through the entire game without understanding which attacks are physical/magical, and to be fair, the game doesn't do a good job of telling you which are which. This challenge might be the only time it's actually necessary to understand the difference in order to succeed.

Anyway, here are a bunch of tips I have:

• Absolute best thing I discovered on my own: Use lock-on mode to ensure that Yuffie will throw her weapon at the box you actually want her to.
• You'll want to take off lock-on mode when mashing buttons, especially the throw/retrieve button since when the box you're locked onto breaks it may chose a random box somewhere else to lock onto and throw your weapon.
• Second best tip: Use the command menu to slow down the game, look at where you want to go next, and lock onto your next box.
• Try not to leave boxes behind until you're in the last room. Break into the last room and get all the time boxes first before breaking anything else.
• Try not to have max ATB. If you can cast a Windstorm on a 1500 box, do it so that you can start building ATB again for the next one.
• For 1500 boxes, you want to throw your weapon at it and listen for two auto-slashes. At that point, the box should be weak enough to finish with a Windstorm. If your weapon can land between two 1500 boxes, you can get them both at the same time. Otherwise, just throw your weapon at the second one after the Windstorm and start moving on and it will get destroyed while you're onto the next area.
• For orange boxes, throw your weapon at them and then retrieve it to destroy them (physical damage).
• For purple boxes, throw your weapon at them, be on the ground, and use normal attacks on them (they are ranged attacks that do magical damage).
• For the area that has a bunch of purple and orange boxes together, throw and retrieve your weapon at all of them repeatedly.
• After going up the first ramp there will be a 1500 box tucked in a hidey-hole on its own. I want to save my Windstorm for the set of two 1500 boxes right after, so I just throw/retrieve repeatedly on this box to destroy it. It gets destroyed after 5 or 6 of those I think.
• For orange boxes with a time box on top, don't hit the time box first unless you really need the time immediately. Hit the middle orange box and then retrieve it. Most of the time, both orange boxes and the time box will be destroyed from that.
• For the final room with many 1500 boxes all bunched together, use a fully charged Banishment on the middle box. The AOE effect will expand out from the box that is being targeted with the attack, not from Yuffie's body.
• I believe for Windstorm to work the way you want it against the 1500 boxes, the weapon needs to be thrown away from Yuffie first. If she's holding it, it doesn't seem to do as much damage.
• When not using lock-on mode, Yuffie will throw her weapon at the box that is most in a straight line with whichever way you're pointing the left stick (her body), not whichever box is closest, and not the box that your camera is aiming at. However, it seems that when both Yuffie and your camera are facing the same direction, you can kind of look up or down with your camera to have her be more likely to choose a box at higher or lower elevation, but it seems finicky. Lock-on is best.
• When the weapon is thrown, you can use ranged attacks on any target, not just the target that the weapon is stuck to. You should be using this to your advantage by throwing the weapon at a 1500 box, then using attacks against nearby purple boxes, then using Windstorm on the 1500 box to get your weapon back.
• Also, remember that your Windstorm can be cast on boxes from long-range. I kept walking right up to them.
• Keep footwork in mind too. Some boxes should just be destroyed from range while moving Yuffie closer to the next boxes.

Extra note:

• I wasted a lot of ATB by not using it in the very beginning. It's sitting full very early.

Questions to look into if you want to get a better time:

• If Yuffie is facing the camera where there are no targets, but there are targets behind her, where will she throw? Does she also attack targets the same way, or just for throwing?
• Does ATB charge the same regardless of whether you're hitting boxes or not?
• Does Yuffie's throw/retrieve combo (Y button) alternate between physical and magical damage?
• What is the penalty for using physical damage on magical boxes and vice versa?
• Most efficient route for ATB?
• Better way to destroy the assorted box area?
• How to destroy the furthest two boxes behind those two moving shields before you even get there (I've seen some people do it while dealing with the assorted box area)?
• Is it faster to run or to dodge roll?
• Does the Deadly Dodge materia change the speed or help with destroying boxes?

My remaining time was 22:55. The best remaining time I've seen someone get was 1:07:10 and he didn't use pause mode (which saves time as long as you're still accurate). He also has the best record I could find for the base game's Whack-a-Box challenge.

Final Fantasy VII Remake Intergrade - INTERmission DLC