At first glance the table rows seem to have different heights:
But if you zoom in, you'll see that they actually have the same height, here e.g. at 1600%:
Thus, the effect you see at 100% is merely a display artifact of the PDF viewer.
If you furthermore look at the page content you'll find:
0.5 w
88.3 803 418.4 3 re
S
0.5 w
88.3 800 418.4 3 re
S
0.5 w
88.3 797 418.4 3 re
S
0.5 w
88.3 794 418.4 3 re
S
0.5 w
88.3 791 418.4 3 re
S
.
.
.
0.5 w
88.3 515 418.4 3 re
S
0.5 w
88.3 512 418.4 3 re
S
0.5 w
88.3 509 418.4 3 re
S
i.e. 99 rectangles with a height of 3 each and a vertical distance of 3, too, with a line width of 0.5. Furthermore there is no transformation or userspace unit definition, so the unit of those dimensions is 1 / 72".
In essence, therefore, the PDF content describes exactly what you wanted, a table of rows each of which exactly 3 / 72" high.
Thus, any display inaccuracy is due to limitations of the PDF viewer, the display device, or any other component involved (e.g. graphic drivers, OS display abstractions, ...)