Repeat these steps to see the problems.

1) Create image 16x16, define 1 pixel grid.
2) Select Pencil tool

3) Create a new brush, shape square, radius 2.0.
4) In tool options of the pencil tool, click the yellow arrow
   (Reset size to brush's native size).
   Result: Size 5.
   Problem 1: Should that be 4?
5) Now draw with size 5, 6 and 7:
   Result: a square of dimension 5x5 is drawn.
6) Now draw with size 8 and 9:
   Result: a square with dimension 7x7 is drawn.
   Problem 2: The selected size does not match what is drawn.

7) Edit the brush radius to 0.6, press "Reset size to brush's native size"
   in the tool option. Result: size 3. Draw: Result: 1x1 pixel is drawn.
   Set size to 4, 5, 6, 7 an 8. Draw. Result: 3x3 pixels are drawn.
   Problem as above.

8) Edit the brush radius to 1.0, press "Reset size to brush's native size"
   in the tool option. Result: size 3. Draw: Result: 3x3 pixels are drawn.
   Set size to 4, 5. Draw: Result: 3x3 pixels are drawn.
   Set size to 6, 7 and 8. Draw. Result: 5x5 pixels are drawn.
   Problem as above.

   The variations are endless.

9) Define a brush, radius 2.0, circle, press "Reset size to brush's native size"
   in the tool option. Result: size 5.
   Set size to 5, 6 and 7. Draw. Result: A "circle" is drawn, the diameter 
   is always 5. At size 7 a solid square 5x5 is drawn.
   Surely it's hard to draw a circle with so few pixels, but neither the size
   nor the shape are correct.
   Problem 3: With circular brushes the selected size doesn't match what is 
   drawn and the rasterization is somewhat sub-optimal.