The meaning of $W=-\Delta U$ has been misinterpreted here. The OP states it as
It means that Work done against a force (or work done on a system) increases its potential energy. And Work done by a force (or work done by the system) decreases its potential energy.
This is false. What this equation means is that the work done by a conservative force is equal to the negative change in potential energy associated with that conservative force. This can easily be seen by using the definition of potential energy and work. Considering a conservative force $\mathbf F$ with associated potential energy $U$:
$$\mathbf F=-\nabla U$$
The work done by this force along some path starting at position $\mathbf{r_1}$ and ending at postion $\mathbf{r_2}$ is then given by the line integral along this path
$$W=\int_{\mathbf{r_1}\rightarrow\mathbf{r_2}}\mathbf F\cdot\text d\mathbf x=-\int_{\mathbf{r_1}\rightarrow\mathbf{r_2}}\nabla U\cdot\text d\mathbf x$$
Using the fundamental theorem of calculus we arrive at
$$W=-\left[U(\mathbf{r_2})-U(\mathbf{r_1})\right]=-\Delta U$$
Therefore, this equation is only concerned with thinking about the work done by conservative forces and how that effects the potential energy associated with those forces.