First off, thanks for the detailed response, it's gotta be a wall of text since I put up a wall myself.
I actually realized after I posted it that there was a whole subforum here and a lot of this has already been covered. So I'll just go over the remaining points.
For the master reports, a little context for the user on how to open the interface would be helpful. Even if it's a temporary dialog with buttons to connect all the UI pieces, it wouldn't be that much worse than the original. Heck, you wouldn't even make players wait 5 seconds for a smarmy AI WAV file to play before displaying the menu, so you're already ahead of the game
I'd be glad to work on some UI connectors to allow localizing out some text and events, that would let you make the code part and people like me could make smaller scripts with the help text and triggers that make them appear. It's not a trivial ask, but I've done something similar in other games and it did end up saving time and being easier to have a simple event thrower/listener than hardcoding the tutorial stuff directly into the game.
For the factory alert, and other stuff, something like an "events scroller" at the bottom would be good. Any event, be it "time travel", "bold new discovery", "factory can't deliver goods" or "no more air" could all show up in a feed. Players click the event to get deeper context and information, and maybe color code and/or flash critical events that need immediate attention. Something that always bugged me about Outpost was that things would happen, from the seed factory imploding to the rebels surrender, and I'd have no idea it happened until I clicked News Briefs. Bringing that to the foreground will go a long way here.
For the materials breakdown, I can see an entire "resource view", that has minerals, metals, air, etc. all on the list. Each has an In/Out column, to show the balance. Clicking any resource shows what buildings are creating, and consuming, these resources. You can get fancy like click an element to move to it on the map, or prioritize/enable/disable buildings that consume resources, but to start with just a list of the things and the balances would solve a lot of problems.
I can mock up a couple of these for you, what's your preferred format?