Summary: The pro-isomorphic zeta function of a finitely generated nilpotent group is a Dirichlet generating series that enumerates all finite-index subgroups whose profinite completion is isomorphic to that of the ambient group. We study the pro-isomorphic zeta functions of \(\mathbb{Q}\)-indecomposable \(D^*\)-groups of even Hirsch length. These groups are building blocks of finitely generated class-two nilpotent groups with rank-two centre, up to commensurability. Due to a classification by Grunewald and Segal, they are parameterised by primary polynomials whose companion matrices define commutator relations for an explicit presentation. For Grunewald-Segal representatives of even Hirsch length of type \(f(t)=t^m\), we give a complete description of the algebraic automorphism groups of associated Lie lattices. Utilising the automorphism groups, we determine the local pro-isomorphic zeta functions of groups associated to \(t^2\) and \(t^3\). In both cases, the local zeta functions are uniform in the prime \(p\) and satisfy functional equations. The functional equations for these groups, not predicted by the currently available theory, prompt us to formulate a conjecture which prescribes, in particular, information about the symmetry factor appearing in local functional equations for pro-isomorphic zeta functions of nilpotent groups. Our description of the local zeta functions also yields information about the analytic properties of the corresponding global pro-isomorphic zeta functions. Some of our results for the \(D^*\)-groups associated to \(t^2\) and \(t^3\) generalise to two infinite families of class-two nilpotent groups that result naturally from the initial groups via ‘base extensions’.