Definitely not permanent substitutes, they may very well exist in the core game - but no guarantee either. Mods exist because a player wanted something different than how the game is at the moment. A great example is @Froggy’s Stonehearth Cafe. He implemented a cook before the devs did (by a few alphas I believe).
One thing to be careful of is “stealing” a mod author’s work. If a mod becomes really popular, it would be unfair for the devs to just stick it into the game, as future players would associate the feature(s) with the game devs not the mod author.
Stonehearth is meant to be modded, so the devs want there to be lots of mods, and want to enable player choice. You (and I) may like to organize our stockpiles to the t, while others just have everything mixed together. Putting it in the core game removes that choice, so some features may only ever be in mods. (No idea about this one in particular)