Man, I'm both extremely flattered you played this much and horrified because the sheer amount of improvements that I've been making from this version is crazy, so I hope you didn't get fed up with the game by the time the new and improved version comes around.
First to address the bugs you shared on your screenshots. I BELIEVE these should ALL be fixed with the next patch since I completely remade the chain resolution logic in order to precisely fix the problems you outlined which I couldn't get fixed by the DD49 release, however, I'll double check with this specific gamestate to see if it's working correctly or not.
The new system also allows for a "Super fast mode" that makes turns go by in an instant, so for veteran players like you it will make future runs way more enjoyable.
I'll address other suggestions and comments in no particular order but I think you'll be happy to hear that most of the things you suggested are coming soon!
First the "Finding the broken strategy" part. In part, I did want players to create broken decks and two-card combos, and there is a small bit of work put in place to prevent it from being TOO easy to achieve, but not that much really. Future updates will feature achievements as you mentioned to push players to try different things, but it will also provide increased challenge on higher difficulties (For example after winning 4 or 5 runs, bosses will have access to tools and logic to stop infinite combos specifically). This should force you to build a more robust deck that doesn't rely on a single infinite combo to win harder runs.
Edit2: Another way to incentivize the player to try different strategies will be the upcoming Equipment system that will give you unique items that modify combat. For example, items that make it so your direct damage spells deal additional damage if your deck doesn't contain any minions. I believe that if the player obtains such an item, they'll have a reason to want to try out such a build either in their current run or on future runs. I'm working on the foundations for this mechanic right now, so if everything goes well it should be running in 2 or 3 weeks with 50 different pieces of equipment planned for the first batch.
Additionally, one feature that I'm heavily debating if I want to add or not (And will probably include an optional toggle at the start of every run) Is limited crafting abilities at the forge. So what effects you have available when crafting will be limited and randomly selected. A higher Intelligence will give you a bigger pool of effects to use at every forge. This should completely eliminate the problem, but it might also eliminate the fun of doing these broken combos, so I'll have to test it a bunch to see if it's a good idea to include it or not.
Regarding adding cards from the pack to the deck, I was actually fiddling with that idea and will probably implement it for the next dd.
Regarding the issue of "upgrades available" still showing after maxxing your upgrades, I'm not gonna lie, I never expected someone to go this far with the demo so I didn't even test this scenario, needless to say, I'm extremely flattered you played it this much.
Edit: I forgot to mention, the problem with not being able to create mods is 100% because of wine since the way I create the file and folders is very windows oriented, I'm not surprised it doesn't work, however a workaround, for now, would be either doing what you did or just cloning the anime mod folder instead of modifying the content of the original so you can have multiple mods at a time (I believe this should work). Also I'll look into the merchant bug.
Regarding your problem with resolution, the options are saved as player prefs, so they are saved in the registry, I have no clue how that would work on Wine, but instead of trying to fix that mess, I can just do a build for you that fixes the settings on startup of the game. Additionally, since you played this much I'd be more than happy to give you some dev builds with the new improvements once I polish some minor issues the current development build has. If you are interested in either of those, feel free to join this discord server and I can send you the special builds there. https://discord.gg/QxyuB8t7
(Also if you don't use Discord which would be understandable lemme know and we can talk through some other platform).