The input in the Minimum-Cost Constraint Satisfaction Problem (MinCSP) over the Point Algebra contains a set of variables, a collection of constraints of the form $x < y$, $x = y$, $x \leq y$ and $x \neq y$, and a budget $k$. The goal is to check whether it is possible to assign rational values to the variables while breaking constraints of total cost at most $k$. This problem generalizes several prominent graph separation and transversal problems: MinCSP$(<)$ is equivalent to Directed Feedback Arc Set, MinCSP$(<,\leq)$ is equivalent to Directed Subset Feedback Arc Set, MinCSP$(=,\neq)$ is equivalent to Edge Multicut, and MinCSP$(\leq,\neq)$ is equivalent to Directed Symmetric Multicut. Apart from trivial cases, MinCSP$(Γ)$ for $Γ\subseteq \{<,=,\leq,\neq\}$ is NP-hard even to approximate within any constant factor under the Unique Games Conjecture. Hence, we study parameterized complexity of this problem under a natural parameterization by the solution cost $k$. We obtain a complete classification: if $Γ\subseteq \{<,=,\leq,\neq\}$ contains both $\leq$ and $\neq$, then MinCSP$(Γ)$ is W[1]-hard, otherwise it is fixed-parameter tractable. For the positive cases, we solve MinCSP$(<,=,\neq)$, generalizing the FPT results for Directed Feedback Arc Set and Edge Multicut as well as their weighted versions. Our algorithm works by reducing the problem into a Boolean MinCSP, which is in turn solved by flow augmentation. For the lower bounds, we prove that Directed Symmetric Multicut is W[1]-hard, solving an open problem.