A software developer's worst nightmare. "When I turn logging on the problem goes away."

It could be that running the game at full speed causes some lock contention that doesn't happen when slowed down by the log stream.
Or it could also be that under normal gameplay your system spins down the harddrive to save power due to a lack of accesses, which would cause slowdowns and choppiness when the game suddenly needs to load something - also something which would be helped by running the log in the background.

For testing the second point, I'd suggest running something like this in the background while playing; (i.e. generating some constant load)

while true; do
  uptime > $HOME/workaround-test
  sleep 1
done

Try limiting the frame rate.

I toggle off my compositor and it makes Warframe much smoother (kde has a default keybinding for it I think)

Have you tried installing Linux?

sounds to me like a timing issue. By using the proton log you might slow down to the point the timing issue doesn't give you problems anymore. Try disabling vsync and enabling a fps limit (warframe has both settings itself).

Another possible cause could be filesystem going to a powersaving mode during normal gameplay and by writing logs you keep the disk in high performance.