I believe we are using the kind of putty that accepts stain. Of course, there will be no wood grain where the putty is.what kind of putty? Stain and putty??????? there's only a few puttys that take stain. most don't.
I always save the sawdust of the material I am working with and mix it with glue and stain to fill... Sometimes just stain depending on whether the glue will bond to the stain...