No problem for the long reply, as you can see from most of my comments I tend to write plenty as well. I'm glad to have inspired you further, I was worried that my comments may have been a bit too much. Funnily enough going through your comment it seemed that most of what  caused problems were the typical dev issues of over-familiarity with the game that I personally guessed were the case (because I've had problems with that plenty of times). The exception to this was the fact that you knew about and prevented a soft-lock that I thought was in the game shows the though put into it accessibility, even if I didn't find it the first time around.

Thankfully, I think that most of the problems will have solutions that you can easily implement, and iterating on what one made in a game jam is a tried and true tradition. I'll keep the game in mind for when you update it

Sure I'd be happy to help. My main email is "rowanfr@gmail.com", you can send me an email there. If you want to send specific builds and questions there I can give you my thoughts. Fair warning though it will probably take 1-2 days for me to respond due to work, but so long as that's alright I'd be more than happy to help.

To answer the questions you have currently:

For the bit manipulation I would do what you suggested and mask it from the user, as most people aren't programmers and that syntax is something that's only familiar to them. Your correct that this would remove a great deal of the puzzle from the user so instead you could add complexity from creating the brew.

Their are 2 systems that I could think off, one which you put which is a tag system or a check-mark system. In essence it checks to see if you have applied certain processes, such as checking if something has been boiled or fermented, or if it's a gas, liquid, or solid. I don't think though that you should tag every element as that would be a lot of memory for every new element. I think tagging fundamental things like it's state or quality, or something else which would apply to many potions is good, but assuming you want a variety of effects tagging all of them would start to consume a lot or force overlap with other effects (such as 111* being confusion and 11** being slowness). One can get around this somewhat by using a priority system where certain effects are evaluated first but I'm not certain this complexity would be satisfying as one can't progress to discovery they instantly arrive at it or fail with no in between. Their is no close solution to what's requested which is really important for helping players learn, similar to most puzzles you want the player to get close to the solution so that they have something immediately to do and then let them work out the harder solution. (Credit where credit's due this idea comes primarily from Mental Checkpoint "How These Puzzles Deceive You" and you can also see a lot of this in GMTK "What Makes a Good Puzzle")

Another example example system would be that instead of a single byte with bit manipulation you could have multiple bytes represent axis in the game which you can manipulate in a greater variety of ways. Such as having 4 axes for fire, earth, air, water which could create a 4D graph (or 2D if you want to make it conceptually easier and have earth/air and water/fire be opposites) where you can have localized regions for certain effects, some positive some negative, which the user has to figure out by crafting brews. To alter the 4 byte brew one could produce something similar to what you have already made, just with more ingredients and more cooking methods which apply effects on those ingredients in systematic ways, such as fermenting amplifying the value on an axis. I think this would likely be fairly easy to implement (famous last words, I know) but create substantial complexity because one could include positive boons which they want to reach and negative side-effects which they want to avoid. The main downside is loosing the satisfaction and efficiency of bit-shifting but I think that if you want to open up a lot of effects you should do something which will allow that. Typically some systematic approaches that the user can build knowledge of to craft more advanced potions is satisfying, which is what made me think of that multidimensional system as it can be easily quantified and shown to the user while still providing complexity but it's not perfect. For one effects like confusion or invisibility will always have difficult recipes because it's hard for those things to have a defined composition of 4 elements, but the useful things about the axes is that one can give small context clues by how the in game character responds to the vector of a potion, such as the potion looks clearer than normal for the vector close to invisibility or upon smelling it gave a mild headache for the vector close to confusion. One could also combine systems like the tag system from earlier and others to make certain there is enough overall meat to the system. Another useful thing is that it becomes easier to add new axes by just adding another optional u8 to the brew struct (one can also isolate certain effect vectors to certain dimensions so that additional dimensions don't negatively effect information gathering for hard effects, such as confusion only being on the air and water axes).

Sorry if the previous 2 paragraphs are a bit large but this is at the core of the game and should be given the most thought as a result, no matter what system you chose to go with. Everything should branch off the core idea of the game which in this case is brewing. The main thing to take away from these paragraphs is not that you should use this multi-dimensional system, but rather that you should think of a system that would make the user enjoy thinking creatively while pursuing a specific goal whatever that system might be. Each brew request should be seen as a puzzle in some fashion, and engage the player as such. Whether it be in the procuring of materials, cooking, bottling, or some other aspect their should always be something that makes the player enjoy solving a puzzle or engage them in some other way (outside of the first few tutorial brews which should hold the players hand a little bit).

The mix of 2D and 3D is good so long as it is what is present currently, that being 2D menus are entirely separate from 3D assets. The main thing most would find jarring is 2D assets in a 3D world or vice-verse unless done intentionally.

For the world map first I would pursue it with time but first I would flesh out a store and have the current solution be you spend some resource at the store to get new items. You can add other systems to get more items such as Recettear where you fight in a quest to get them but I think creative generation of unique brews is this games focus, not questing or world exploration, so I'd leave that on the back burner until the main loop is finished and start with the simplest implementation of a shop's expansion.