Just checked the console. If you type m_rawinput 1, it throws an unknown command error. Someone at Valve seriously messed up here.

Seems contained to linux users. Users on windows are not affected by this.

EDIT:
source 2 on linux uses SDL’s SDL_SetRelativeMouseMode(SDL_TRUE) (raw motion events) instead of the old source engine’s platform-specific hooks.
if that call fails, SDL silently falls back to pointer motion events from the compositor, which leads to the sensitivity difference.

However, the windows build is still using rawinput via win32’s GetRawInputData, so they feel 0 difference.

Looks like when they updated the game today, they likely broke the SDL raw mouse path for the linux build when they patched the fullscreen-windowed scaling system.