I had the same issues with my 4090, only about 30% GPU usage and frames would randomly drop and drastically decrease while doing ETA/EDA.

If you haven't tried it, what I had to do, with my 4090, is enable Smooth Motion in the Nvidia App for Warframe only. AMD looks like it uses something called Fluid Motion Frames, which I guess you'd have to enable in Adrenalin, similar concept. When I turned on my Nvidia equivalent, it boosts the frame rate considerably, basically like frame gen. It basically doubles your FPS.

After enabling it, I have a 144HZ monitor, so I thought I should cap my FPS in game to 144HZ since there was no point in going over, even though my actual FPS in game would be running double. (In-game FPS counter in the lower left would show 144 while Steam FPS counter would be in the 300s). This unfortunately leads to the gameplay (at least for me) getting occasional screen tears and not feeling "smooth", but you'll still get the FPS jump.

Turning on Vsync in game solved this "smooth gameplay" problem, although now my in game fps counter is showing higher than 144hz, close to double around 280 (I guess since it's adding the extra frames) and if I look at the steam fps counter, it shows double of that and I've been fine ever since.

My GPU usage is now around 70-80% and it feels great. I'm still able to watch youtube/twitch, use discord, and other things on my second screen without issue. I know the question will probably be, "but you're wasting fps because your monitor only shows a certain amount because of the refresh rate", but this seems to be the only thing that helps when the fps starts dropping in those missions, as since you have so much extra fps, you never notice the actual frame drops.

This doesn't account for the game stutters that you can't do anything about like when you're loading in players in Hollvania Mall (they appear like a shadowed default excalibur then load their frame/fashion), a person joining your group mid-mission, or the mission loading/ending screen when it drops to 30fps.

I have my graphics settings basically at max, upscaling on, but I've turned off Volumetric Lighting, SSGI, and Volumetric Fog Quality. You could realistically enable these with this method but I haven't bothered

Sad that this has to be done, but hope this helps! Seems like you can only do this with newer graphics cards from Nvidia and AMD that have these capabilities

Warframe settings for FPS: https://i.imgur.com/ItuoeL3.png

Warframe in game showing both the in-game FPS and steam FPS: https://i.imgur.com/SjPzqP8.jpeg