Dewey,
You are correct. Tensile strength can be accounted for by hardware selection. The problem is that the aluminum aircraft structure becomes the anode and corrodes in the presence of stainless if an electrolyte is present if the two metals are not electrically isolated.
Even more of a concern in coastal areas.
An easy way to spray paint screw heads: Clean the screws first in a jar with appropriate solution (acetone, MEK, thinner, etc.), allow to dry, drill holes in a piece of cardboard, insert the screws and paint. Chances are you can get quite close to original paint color with appropriate inexpensive rattle can and won't notice the color difference if it's close. Better if you have some original color lying around. Install the screws by hand after they have dried and you won't muck up the new paint.
Good luck,
Vac