Hey, thanks for this very detailed bug report, we will be working to fix these as soon as possible.
Regarding the maps: in the 0.7 update we will be using a whole new system (that we are currently developing) to make procedural dungeons, and there we will fix most of the issues with the dungeons, including the pathfinder, the lighting, etc.
Little spoiler but, there is a Feature planned for the launch of the game, a whole mode where the objetive is to pursue the subs and get back at them!
Thanks for your report and ideas, i love when people share such great posts as you!