On the one hand, one way to eliminate the contrast problem is to use sawdust from the wood you're working on. Make a small pile, add some tung oil, and drop in some stain. Mix it thoroughly and fill the nail holes with it. You've got to play around with it a little bit to get the right color. The tung oil acts as the binder that holds the sawdust in the nail hole.
Windows pose their share of application problems.
They can become very labor-intensive if they have small glass panes and lots of mullions, since extra time and care is required to keep the coatings off the glass. Anderson, who sprays coatings on windows, cuts down on labor requirements by using a spray-on liquid mask, Trimex, that peels off the glass easily. It's a clear primer and sealer. A final word about shellac. With the concern over VOCs, it's difficult to find fault with a product that comes from bugs.