Don't you normally see the "impact" alert before you hit something and get the flashing cockpit lights?
Never hit a capital ship so not sure how that would work. Is that only for things like asteroids and planets/stations?
Whenever I've run into the hitbox of a cap-ship it's always been much like the OP's video.
Your shields start to take hits depending on your position relative to the hitbox and then deplete fairly quickly.
Must admit, whenever it's happened to me it's been when I was "sightseeing" so I've just reversed back the way I came before I started to take hull damage.
Can't say I've ever noticed the proximity lights flash though.
Maybe the lights are keyed to the actual ship, itself, so if the hitbox is out of whack you don't get the warning?
Last time it happened to me was when I was trying to get selfies with the cap-ship in Merope.
I'm out that way now so tonight I might see what happens when i try to get close to it again.