Hi,
I don't think that Mathematica prints the disks with radius one. You are creating two different graphics objects, the axes of which are scaled to render the disks at their "optimal" size. If you plot them into one figure you see that they indeed have radius 0.01:
Clear["Global`*"];
Graphics[{{Orange, Disk[{0, 0}, .01]}, {Black, Disk[{2, 0}, .01]}}]
produces this image:
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Cheers,
M.
