I want to thank you all for your great and detailed feedback. Like I said in the original post, I'd like to keep working on these options as we continue making the game so that we can meet everybody's needs as much as possible.
I've been working this week on expanding functionality, based on your posts. Upcoming changes in the testing branch include:
Rooms Overlay: I looked into giving different room types different patterns (striped/dotted/etc) but this turned out to be quite a huge change. Instead, I looked at the different room types which would need to be most distinct from one another and made colour changes which push those further apart from each other. I think what I've landed on is pretty decent, but I'd be very interested in your real-world experiences with it. Even for the default colour mode, this overlay is more of a "colour carves out space" mode rather than a "colour shows full info". That's something I'd love to fix for both cases, but in the meantime let me know if these options are any better.
Germs Overlay: Colour choices are more distinct from one another. I also would have loved to use different patterns/textures for each germ type! But, now the old similar-looking ones should at least be more readable.
Power Overlay: Strained and Overloaded colours are more distinct from one another. As well, I made the colour of the "power generator" icon a bit more vibrant so you don't get the muted, dull version.
Light Overlay: Change the light colour to a more vibrant colour. I found it a little tricky to read light levels on low-light tiles even in default mode, so this is done in default mode as well as deuteranopia/protanopia.
Tritanopia Mode: I have made a Tritanopia mode but this one is a lot harder for me to test. I've been using a Deuteranopia/Protanopia simulator to check all of my changes, but the program I'm using doesn't have a Tritanopia option. I will look into a Tritanopia simulator so I can check the stuff I've been doing @Harryy -- I don't feel super confident putting the mode out without confirming that the changes I made even help!
These should be live on Monday if you'd like to check them out and let me know what you think. I'm going to continue working on this stuff for a while yet in this batch, to try and catch more of your notes. Cracking open the Temperature Overlay and Plumbing Overlay now -- I love your idea for the temperature view @GonDragon, so I will probably start there Thanks for the tip!
I considered this, but I wound up not doing so because I didn't want to complicate discussion of automation between players. That said, there is certainly some dissonance when looking at a wire being described as Red when it doesn't look Red... this is a tricky one -- if y'all feel strongly about it we can reconsider.
I want to reiterate that I'm extremely grateful for your help and feedback here. It means a lot!
[edit 06-19 night: I snuck in the changes to the Harvest Tool as well! That will be in the Monday update]