Physical design systems (modeling possible boat hulls, say—not the physics itself but the interaction of numerous variables) and resource allocation (drafting a baseball team, say) seem like other likely areas, though I’ve got no idea if constraint tools are the best option or whether they’re even used.
Broadly: if a multivariate problem can’t be modeled, a constraint-based search strategy is the(/one) next-best tool.
I don't think MiniZinc itself is used by any package-management tools, although some use competing tools/libraries. Personally I've used MiniZinc for a related problem: finding a subset of dependencies (of a given size, say 10), which satisfy the most outputs.
Edit: Another constraint modelling problem I've tackled (although I didn't use MiniZinc to solve it) is seating allocation on public transport: if the scheduled vehicle is unavailable, and the replacement has a different seating layout, how can we best assign the reserved seats (taking into account ticket class, seat direction, window/aisle, amenities, etc.)?
Sophisticated programming languages dive towards this direction already compared to untyped cousins. Programs are validated against type theory correctness. You can go deeper with dependent types. And those languages go all the way down to prove everything there is to be proven.