A GSW to the brain has direct effects and indirect ones.
Depending on the ballistics surrounding the projectile, significant direct damage will occur to surrounding brain tissue from the shock wave which spreads out from the projectile path. Obviously tissue through which the projectile passes is also destroyed or torn or otherwise disrupted.
There are two major types of indirect effects I can think of.
First, this sort of trauma produces a secondary swelling of the brain tissue itself, into an enclosed cavity. We can do an assortment of things to help this, and this pressure is always monitored carefully. It’s not unusual to remove part of the skull and not replace it for some weeks, to allow for expansion of the brain. If the brain swells too much into an enclosed space, it’s blood supply is compromised. There is also a pressure increase which can occur from bleeding. Again, an enclosed space, so active bleeding compresses the brain either inside the brain or between the brain and the skull. We can usually fix this, but of course you sometimes damage some of the brain getting to an area of bleeding. Regardless, any secondary swelling is damaging to the brain even if you control it at a gross level. There are a bazillion little connections in there fairly delicately wired.
The second kind of indirect effect is disruption of pathways. The brain likes to talk to itself and is pretty interconnected, so you might have an effect over here that disrupts an entire process which might be considered to be located over there, but actually uses pathways and/or processing information located over here.
About your buddy Phineas. Back in the day when men were men, right, although I think I’ve read about primitive societies that went about chopping into skulls and the “patients” obviously survived based on the fact that the skulls had healed…
Anyway, a bar of iron (if I remember the story) punched through his frontal lobe. He ultimately did fine, except that he had some personality changes and I think he eventually checked out from seizures (a common sequela of brain trauma). Well, basically that’s a low velocity mechanical punch through the brain, and since he only lost tissue from a (reasonably) “silent” area, and didn’t croak from infection or hemorrhage, it’s a pretty simple explanation as to why he did “fine.” Of course, no part of the brain is actually silent (the 10% use assertion being a complete canard), so it’s better to say he didn’t lose anything real critical to seeming like he was a regular guy. I suspect someone meeting pre-accident Phineas might not be so impressed that post-accident Phineas was “normal” compared to the original.