What you're describing is the dissonance between having a normal human (with all of the common context that carries with it, like "people often die when they are shot at all") as the final boss and the expectation of a final boss fight being a prolonged, memorable, and epic battle that tests the things you've learned so far. There are a number of clever and reasonable ways to work around these conflicting concepts. Here are a few general methods of doing this that I thought of off the top of my head. This list is by no means exhaustive.
We build the encounter to make it difficult to reach or attack the boss directly. The boss could have mostly-similar stats to ordinary grunts when engaged directly, but the boss constantly summons allies or obstacles. Chasing the boss while ignoring the external threats would quickly result in the player's death, so the challenge becomes controlling the reinforcements while chasing the boss down and striking when the opportunity presents itself. Another possibility along this method is to have a multi-phase fight where the boss is not initially vulnerable, and the player must tackle the different phases in order to open the boss up and make it vulnerable.
We can also make the boss do something to alleviate its human fragility, e.g. get into a mech suit/tank/giant death machine, mutate into a monster, or was never human to begin with - a demon, an alien, a monster, a robot, an angel, a dragon, a dinosaur, a god, whatever. With a reasonable in-universe explanation to why the last boss no longer has all of the normal human fragility, we don't feel the dissonance anymore and can happily fight a boss driving a scorpion tank with accompanying sonic cannon and acid drone swarm.
A third approach is to change the parameters of the encounter so it isn't just a fight. The final mission could be, for example, to infiltrate the final boss's lair, assassinate the final boss, and then successfully extract from that lair. The final mission could be obtaining/destroying the McGuffin that the player and the enemy have been chasing over the course of the game. It could just be "survive long enough" while something happens, like uploading evidence to expose the bad guy's wrongdoing to the world.
As you can see, there's a lot of possibilities to make engaging and different final boss encounters. Not everything has to fall into just standing and shooting each other until one side runs out of health. If we change the parameters of the conflict, we can make the encounter different and interesting. We can do this by adjusting other parameters within the fight, changing the boss's state to alleviate human fragility, or even change the goals so that the boss encounter is more than just a gunfight. As a design exercise, can you think of other methods of a final FPS boss fight that maintains the boss's humanity but still makes it reasonably engaging?
Got a burning question you want answered?