After some discussion with the OP, I think we've gotten to the root of the matter. That is, a finite topology $T=\{U_1,\ldots, U_n\}$ is a finite collection of open sets. Then we can discus the "complementary topology" $T^c=\{U_1^c,\ldots, U_n^c\}$ which is a collection of closed sets (closed relative the the topology $T$). However, we could easily have started off with $T^c$ as our topology and gotten its complementary topology ${T^c}^c=T$. Hence, in some sense, distinguishing between open and closed sets is arbitrary since a finite topology generates a collection of closed set which are also a topology, and that topology will generate the original topology as its collection of closed sets.
As the question has now been edited: Yes, there is a distinction between open and closed sets in that open sets are members of a particular topology. However, the collection of closed sets for a particular given finite topology is also a topology.
You get to decide which sets are open as long as your topology obeys the rules of topology: (1) the empty set and its complement are both open and closed; (2) finite intersections are open; (3) arbitrary unions are open.
It could be that all sets are both open and closed in a particular topology, e.g. the trivial topology $\{\emptyset, S\}$.
You will still have limit points, it's just that likely a convergent sequence is eventually constant.
For example consider the topology $\mathcal{T}=\{\emptyset,\{0\},\{1\},\{0,1\}\}$ (the set of all subsets of $\{0,1\}$). All sets are both open and closed.
Consider what happens when we remove a set to form a new topology: $\mathcal{T}_{0}=\{\emptyset,\{1\},\{0,1\}\}$. Now the set $\{0\}$ is closed but not open. The collection of closed sets is $\{\emptyset,\{0\},\{1\},\{0,1\}\}$. These sets are closed with respect to the given topology.
To answer your question:
The distinction between open and closed is not a matter of convention, per se, nor are they "opposites" or "qualitatively different". The distinction between open and closed is a matter of guaranteed membership in the topology of the former. You are correct that for a finite topology, the collection of closed sets will also be a topology.
In the topology $\mathcal{T}$ above, all sets are closed and open, therefore they are neither opposite nor qualitatively different. In the topology $\mathcal{T}_0$, there is one set which is closed but not open. It is kind of the "opposite" of an open set (in that it is a complement of an open set), but it could be argued as being qualitatively identical since it is just a discrete set, a singleton.