I can confirm this bug does happen. I am able to reproduce it with the following setups:
Steam Deck with default configuration
Windows 11 Desktop using Xbox One Controller (Type-C model) - I launch warframe using Steam Install. System specs are Ryzen 7 5700g, 32gb ddr4 memory, Intel Arc A770 16gb video card, 2tb nvme storage.
GPD Win Max - Built-in controller breaks at this point requiring you to use the integrated keyboard to finish the quest.
To work around this issue you need to connect a Keyboard and Mouse to the device in question so you have access to a physical "E" key when you get to this portion of the quest.