In FO3, there appeared to be a damage penalty (20%?) for shooting an enemy with a gun without using VATS. Is shooting an enemy equally damaging in or out of VATS in FO4 ? Thanks!

Judging by single shots with a sniper rifle I would say, yes there is.

On the other hand if you are close to a target, shooting rapidl without V.A.T.S seems more effective.