I've only dabbled in herbalism, and alchemy in the crafting for the module. I don't have any comment on herbalism, since it has had changed since I was last doing it.
For alchemy, and making varnishes, I will say the latter stages working towards "mastery," isn't particularly fun. As I touched upon in the other thread, not being able to bulk turning essence into varnish is dumb. In my experience, the DCs for refining are lower than working the raw materials, so you stop getting exp for making the finished product. Therefor, being able to bulk them, or not, does nothing to effect the speed towards mastery, the limiting factor is the scarcity of raw resources.
I would say either allow players the ability to bulk the finished product, or adjust the essence to varnish DCs to give crafting exp in order to justify the intentional single clicking.
Sure, varnish are useful, but the return on gold isn't great, especially for players who are at a point where they can obtain the later raw reagents. Odds are they can make better money doing other things. At times, I have let 30 + essence go to waste simply because the time it takes to refine wasn't fun, and how I wished to spend my time. I'd say that's not good design.
Not many people wish to sit, and observe you make varnish either, so there isn't much RP to be had, to help the time go by quicker. Plus there is so much clicking while doing it, due to the one at a time way of things, the responses I feel I can give are not the most...descriptive, enlightening, or creative.