It is also depends on the OS. On my MacBook Pro

disk = Graphics[{Black, Disk[{985, 1030}, 600]}, 
   ImageSize -> {2048, 2048}];

ImageDimensions[disk]

returns

{4096, 4096}

So, different behaviors on different systems and different OSs certainly cause problems...

I understand what you are doing, I am doing the same thing and adapting to this chance was annoying ...

You can set $ImageResolution = 72 at the beginning of the session.

Alternatively, you can make all rasterization explicit, and set ImageResolution -> 72. This is some trouble because I also used to do things like Binarize@Graphics[Disk[],...] instead of using Rasterize explicitly.

I have not refactored all my code for this, but I was thinking of using something similar to the following:

rast[im_?ImageQ][gr_Graphics] :=
 Module[{w, h},
  {w, h} = ImageDimensions[im];
  Rasterize[
   Style[
    Show[gr, PlotRange -> {{0, w}, {0, h}}, ImageSize -> {w, h}],
    Antialiasing -> False
    ],
   "Image",
   ImageResolution -> 72
   ]
  ]

Then if we have an image im = RandomImage[{0.9, 1}, {100, 100}], we can rasterize corresponding masks as mask = rast[image][Graphics[Disk[{50, 50}, 50]]].

I am curious how others handle this.

See my answer here:

https://mathematica.stackexchange.com/questions/219227/unexpected-behaviour-of-imagesize-and-imagedimensions-in-12-1/

Note that ImageDimensions works on Image and not on Graphics. When you apply it to graphics, they get implicitly Rasterized. 12.1 may rasterize at higher resolution, depending on the screen you have connected.