Glazing takes a long time to cure and in my opinion is not ideal for nail filling, though it works and I have used it. DAP actually makes a product that acts a lot like glazing but with a faster dry time, called Painters Putty 53. Still, it wants 24-48 hours before applying paint. Glazing (read the can) wants to have a firm set (can be several days to weeks) before applying an oil-base paint or primer. I think you are doing your customers a disservice if the manufacturers recommendations are not followed.
I like Elmer's wood filler for nail holes inside and out. There is an art to filling the hole and smoothing it over so there is very little if any sanding necessary. It will rewet with dew or rain, but can be coated within 15 minutes with latex or oil. From your post, it seems like you think the wood filler does a nicer job.
But in the end, it's different strokes for different folks (where is he?). 30 years with no complaints is good enough testimony for me, but I like my methods-- they are efficient enough for profit and provide quality, IMO. It's usually not worth arguing about. If you're the boss you tell them how it's going to be done, end of story.