After seeing this I'm going to say that you should probably put the warning message before encounters back in. Leaving it out is going to cause a lot of YASDs.
You still can't move if the alarm is up... if I do change it back, I'll want it to work differently. Show up only after the actual enemies are visible, and say something a bit different depending on the context.
Yeah, you can't move, but how many of us have gotten their characters killed because their finger was stuck on the 'wait'-button for a little bit too long? Ideally the announcement should prevent all further repeated keypresses until the player stops pressing down the current key.
You could have an option on the main operations screen to activate/deactivate it. If I'm about to enter an area where I suspect to get involved in a fight, I'll be sure to have it 'on'. Otherwise, I probably don't need it and turn it 'off'. Seems easy.
Also - And I don't know why I haven't noticed this before, because I
always play on Nightmare Mode - the introductory text for a Nightmare Mode game should perhaps mention that the Arch-Conservative nutcase already had their first term with which to wreck the country. That would better explain why every law is deep red at the start. Right now, the gameplay is kind of divorced from the story in this case.
Watching your first video also made me wish again that the 'Dodge'-skill would still give a bonus to firearms evasion, just a much smaller one (maybe a third of the melee value?) than in earlier versions, where it really did make you invincible.