There are two ways to reflect a vector $v$ by another vector $u$. The first is to 'directly' reflect $v$ through $u$:
where $v'=2P_uv-v$ with $P_u=\frac{uu^T}{|u|^2}$. The second way is to reflect $v$ through the normal plane spanned by $u$ like this:
This time the reflection is $-1$ times the other convention i.e. $v'=v-2P_uv$. To me the first way seems more intuitive but if I look at this article https://en.wikipedia.org/wiki/Geometric_algebra#Reflection they use the second convention. Is it common in math to use the second convention? Are there any benefits compared to the first convention?



Reflection typically means “I have an eigenspace for 1 with dimension $n-1$ and an eigenspace for $-1$ of dimension 1”. The former eigenspace is the hyperplane, the latter is the subspace spanned by the normal.
It seems to me the reason you think the two are similar is compounded by the fact your example is in 2-d.
The first example you are giving is “reflecting through a line.” This works in 2 dimensions, but in $n$ dimensions, if you reflect all vector across a fixed vector in the plane they generate, you can get something else, namely a rotation. I hesitate to call this a reflection but as it happen some authors (see last big paragraph of the lede ) are willing to admit any nonidentity involutive isometry with an affine eigenspace for 1, of dimension less than $n$ as a reflection.
The choice of thinking in terms of the hyper plane or its normal are both still there in $n$ dimensions, but the different “nature” of each type is a little more obvious. Each one has the data needed to determine the other one. This is a duality. But they are only both lines in 2-d.