Our first result realizes the toric variety of every marked chain-order polytope (MCOP) of the Gelfand--Tsetlin poset as an explicit Gröbner (sagbi) degeneration of the flag variety. This generalizes the Sturmfels/Gonciulea--Lakshmibai/Kogan--Miller construction for the Gelfand--Tsetlin degeneration to the MCOP setting. The key idea of our approach is to use pipe dreams to define realizations of toric varieties in Plücker coordinates. We then use this approach to generalize two more well-known constructions to arbitrary MCOPs: standard monomial theories such as those given by semistandard Young tableaux and PBW-monomial bases in irreducible representations such as the FFLV bases. In an addendum we introduce the notion of semi-infinite pipe dreams and use it to obtain an infinite family of poset polytopes each providing a toric degeneration of the semi-infinite Grassmannian.