Thanks for the feedback!
I am working to avoid the typical loss scenario since I also noticed it kind of ruins the perma death. My plan is to only have a some of your soldiers randomly die at the end instead of all of them. I will also play with having all of the soldiers kept alive and look into some other consequences as you mentioned.
You're second point is something I didn't really consider, but it makes a lot of sense. My original plan is to continue ramping up the difficulty of missions so you never feel too over powered, but this will require a large amount of upgrades and levels, as well as a TON of work balancing. Your idea of temporary upgrades could definitely work, but my concern is that it would be difficult to explain to the player and may feel pretty unintuitive or it may defeat some of the spirit of upgrading your permanent towers.
I will definitely try exploring the idea though, as well as brainstorm some other possible solutions.
Also thank you for bringing up the font. I did feel it may have been hard to read in some places but it's good to hear from someone else.