You can use a Predefined brush tip instead of an Auto brush tip for your pixel art brush presets.
e.g Make a 9x9 canvas with a white background and paint five black dots on it in a horizontal line as dot-space-dot-space … etc.
Use an odd sized image for centring accuracy and placement.
Save that as a .png file then put it in the brushes folder of your krita resources folder.
Do Settings -> Manage Resources -> Open Resource Folder to find it.
Restart krita and choose the Pixel Art brush preset and open the brush editor. Choose Brush Tip -> Predefined then select that brush tip that you made, it should be there for use.
Choose a size of 9 and a spacing of 0.1 then paint with it.
You should find that you can do this with three strokes:
You can make any pattern of pixels you like in the .png brush tip file.
If you make a different sized .png brush tip file, use a tip size of the same size as the .png file and a spacing low enough to give a continous line.
Changing the size gives strange results that I can’t figure out.