Update: I've gotten a response from support, and the steps below actually fixed my issue. Specifically the part where you verify + optimize the download cache, and clear the below mentioned files from Warframe's Local Appdata folder.
I am now running more or less smoothly on DX12, the weird flickers seem gone for me now.
EDIT: Shortly after I made this post, I noticed flickering in certain menus still, but it's far more subtle now and I haven't gotten "flashbanged" yet. An improvement to be sure.