...start by mixing up a small batch of filler, and squeegee it onto the wing (or whatever) with a plastic bondo spreader...

The problem I and others have had with that approach is that the filler does not wet out the surface of the pinhole very well. Even though it fills the pinhole, it does not establish a bond with the surface. Often, the pneumatic pressure of the air in the pinhole forces the thick filler back out, so you get only a very shallow fill over the top of the pinhole.

As it ages and the wing (or whatever) flexes, the filler is likely to break free from the interior surface of each pinhole. Then the pinholes start mirroring through the finish paint, and eventually might start cracking in a checkerboard pattern.

Squeegeeing on a couple quick skims of runny epoxy helps wet the interior surface of each pinhole, and forms a rounded meniscus over its sharp irregular internal contour. Filler sprayed or squeegeed over the epoxy skim has a better surface to bond to, and there is less internal volume in each pinhole for air that repels the filler and impedes the bond.

--Bob K.