Is there any particular protocol for the engine compartment brace when lifting or placing the car on jack stands? I.e. under any conditions should it taken out?

 

IMO, as long as you have the car ALREADY in the air symetrically (i.e left and right front; and/or left and right rear) youshould be fine....Never ever jack up the car with the brace out, it will crack your windshield and might bend the unibody. (not sure about the unibody part, but ws for sure)

 

What he said. If you are moving the car up, down, left, right, etc. you want the cross-brace installed. If the car is stationary the brace can be out.

I don't think it will bend the chassis if you lift the car w/o the brace. But, braceless lifting has resulted in cracked windshields.