Cover the icons with your thumbs and it's obvious the boxes are, in fact, changing

Thank you!

A door may have a "level up" buff applied from another object, so one approach could be to find a different entry point (by moving around in the 3d space) and then disabling the buff, as another example.

Yep! There will be a number of hacking tools that will affect the game world in different ways. Which tools you use and put upgrades into will alter your approach. The Unlocker will unlock things, if it's a matching or higher level, however a Corroder will lower the level, for example.

I literally gasped