The game has been "In Dev" since pre-covid. I own a copy and am curious given it's release was Feb 2021 according to the store... (could swear I bought my early-access one sometime around summer 2019.) Steam claims it's release in 2020.

Has there been any software update?
Have the blacked out skill tree options become available?
Has the Custom Character creation been rounded out or made ready to release?

I think I've cleared the initial levels and town only once out of a few dozen plays, and was also wondering if a difficulty selection may have been added.

Yes the game is still in active development with the next major release coming out in the next month or two. The Stoneshard wiki keeps a Development roadmap which tracks the changes and the image on the right covers the major update schedule.