Feel free to let me know if I am missing something that is already implemented?
Well, it may not be a readily available functionality, but I suppose it should be Scriptable without too much difficulty.
I have to go item by item adjusting the sizes individually
Are you using Actions to streamline the process at current?
I have looked into a Script for the task based on the selected layers and so far the best I could come up would still play havoc with the history; though it might be possible to avoid that.
I suppose an easier approach would be to handle all layers within a Group – would this be useful to you?
So all your squares need to be upscaled by precisely the same amount? You can can record an Action that will perform the scale on the first. Then just re-run the Action with a shortcut on all the other layers, you can even automate the "move to next layer" step, so just hitting a single key will transform as many layers as you want one by one very quickly. Transform again (command shift T) will misregister them unfortunately.
Another option is for you to have set the squares up as instanced Smart Objects (if they are all the same). Then scaling one object in Image Size will scale them all instantly.
What you asked for is an interesting request, but its hard to see how it would be useful generally.