For the secret room subject, one way you can bring in secret rooms without altering the current map generation too much is to have it generate walls with subtle hints opening into clickable stairwells, having the secret rooms be completely separate maps to load then be generated along with the dungeon level.
Could also make them time based or have some other hazard in them to keep the dire eldritch danger intact, say some creeping horror slowly consumes the hidden rooms forcing the player to kill what enemies they can and retrieve what they may before getting out for the room to be sealed up afterwards.
Sorry if I'm being a bit bold suggesting all this.
As for the alchemy, sounds perfect! I'm guessing the beer and wine are the ingredient you were considering to add to the mix, or to be part of it.
Nothing wrong with suggestions. Sometimes I get good ideas from those when I'm stuck by giving suggestions a spin and end up with something completely different I wouldn't have thought otherwise.
Secret rooms being separate maps would work perfectly. I'm probably adding some sort of vault system as well at some point so that could work for it too. I've been also thinking about those hidden areas for extending the dungeon for optional branches.
On that note, I'm probably at some point extending the main game as well. I already know how the plot would continue, but I'm still struggling if it will thematically fit the game.
Alchemy would be basically blood + another ingredient like leaves or something similar to that. But mixing beer and wine isn't a bad idea as well. I'd probably add another alcohol type, spirits, so there'd be some variety.