I can understand where your recommendation is coming from. I am not sure it is an easy change to adjust the file structure in the program without a major rewrite of the way it handles recipe archives.
The way BeerSmith is set up, each recipe (and associated brew session) is a self-contained archive (almost, there are a few global settings which should IMHO be included in the equipment profile, such as grain absorption rate). The separation of separate brews from the base recipe is generally what the 'brew log' function intends to do in BeerSmith. It contains the brewed recipes and brew sessions to separate them from the initial recipe.
The way I manage this is to set the date for each of my base recipes as 1/1/2001 in the recipe folders where they are stored. This distinguishes them from any brewed recipe which then contains a more valid date stamp. I copy the recipe using the 'copy to log' button where I can then make any last minute adjustments, update the %AA, prices, and add my water and water adjustments before setting the brew date. I can then brew the recipe using this copy in the brew log to enter in the brew day and finished beer data.
While this is not as neat or clean as having a base recipe and attached brew sessions such as in Brewfather, it does help with tracking a recipe over time and individual adjustments made to the brewing sessions.