Update on the situation:
First of all, I'm running Ryzen 5 5600 with RTX3060 and 16gb ram. Currently I only have problem with Warframe and no other game or program. I tried all the standard things, like drivers update, optimizing/integrity checking etc. before posting here, I wouldn't bother you guys if I hadn't, but thanks for your concern. I was having crashing and heating problems personally, my friends experience FPS drops (their configurations vary, but none are older than three years). However I did some tests and discovered something peculiar about some of the settings...
Sometimes when I change some particular settings, after hitting confirm the game freezes for half a second, and sometimes it goes smoothly back, independedly on what it was set before. If it goes smooth it will crash. Usually within 10-15 seconds of wandering on the ship, sometimes have to start a mission and usually it crashes within first minutes, then. If that slight freeze happens it will not crash - or at least that setting seems to not cause crashing anymore. It happens mostly on: Shadow Quality, Dynamic Lighting, Velumetric Lighting, Local Reflections, Volumetric Fog Quality and Glare. After setting and confirming with all slightly-lagged attempts, it stopped crashing all together for me, tested on two hours of gameplay. Could it be that sometimes, when you confirm the changes, the game fails to load the correct setting pool, maybe loads it partially, and then when it's needed to happen it crashes?
Also, as Psianide73 sugested right, I should have posted some screenshots on the effects, so sorry for the late update, but here they are:
Pseudo lens flares (Is there a way to erase these?):
And about the darkness, it seems to be happening mostly, but not exclusively, in Sanctum Anatomica tileset. That tileset also has problems with colors being faint, while white and black are very strong, examples below.
Thank you once again everyone.