the stonemason stand, woodworking bench and glass forming stand were indeed disabled, which means they might still be present in older savegames, but anyone who starts new game from now on won't have them available.
Lot of same things in the techtree were crafted differently so we wanted to adjust that and after reaching blacksmith station, new recipes were unlocking more randomly without creating some bigger groups. Now the techtree should be much more structured into logical groups creating few eras, while there is always some kind of threshold technology that player needs to master in order to progress further. We will definitely work in the future to explain those informations to players in better way than it is done right now.
You may also notice that kiln now works differently (before it was used only to craft charcoal), and we've introduced some new workstations like chemistry station, locksmith table and ylandium refinery.
We hope those changes will make the crafting more understandable, at least after the period of getting used to them ;-)