This is an epic game so far, although I agree with DarkMirror that the dock is kinda useless right now, so I came up with an idea for how the dock could be used to repair your boat:
TL;DR: You'd only be able to repair your boat up to a certain amount of points and have a limited amount of points to use to repair your boat, e.g. only up to 4/5 points with 6 repair points max. You could use that to add different difficulties with different amounts of points per difficulty. There are several other ways to change the difficulty however, such as changing boss damage, speed or damage resistance/health, although those might add too much complexity to the game. There wouldn't be much of a need for a safe zone around the dock if repairs were just as simple as spamming E once you dock.
Full post:
It's as simple as it sounds: you come back to the dock and can get your boat fixed. However, there are some conditions to make it not too overpowered. You can either A) only repair it up to a certain point, B) have a limited number of points you can use to repair it, or C) a combination of the two.
For example: A) You can repair your boat an unlimited amount of times, but you can only repair it up to 3 points out of 5. (That still might be too overpowered, one of the other options would be better.) B) You can repair your boat up to 5/5 points, but you only have say, 8 (or less) points to use. C) You can only repair your boat up to 4/5 points, and you only have 6 points to use.
I like option C the best. It gives you the option of fixing your boat while being the least overpowered in my opinion. You could also use this to adjust difficulty, where the example I listed is normal mode, easy would be 4.5/5 and 7 points, hard would be 3.5/5 and 5 points, extra hard would be 3/5 and 4 points, and daredevil would be no repairs at all.
In addition to the repairs to adjust difficulty, you could also make the boss to more or less damage depending on the difficulty, or maybe the boss is a bit faster or slower depending on the difficulty, or maybe the boss takes less damage depending on the difficulty. Again, all that might take away from the nice simplicity of the game in its current state.
I'm debating whether or not to make the dock a "safe zone," where the boss will not attack you while you're within a certain range of the dock. Perhaps you could make it so that if you attack the boss while in the safe zone, that zone becomes unsafe and the boss will attack you, plus you can't land a critical hit while in the safe zone. That would be too easy of a way to do a ton of damage.
I think a better idea instead of the safe zone is that the repairs are super fast so that you could just dock, spam E, and then leave.