Logical gates constitute the building blocks of fault-tolerant quantum computation. While quantum error-corrected memories have been extensively studied in the literature, explicit constructions and detailed analyses of thresholds and resource overheads of universal logical gate sets have so far been limited. In this paper, we present a comprehensive framework for universal fault-tolerant logic motivated by the combined need for platform-independent logical gate definitions, flexible and scalable tools for numerical analysis, and exploration of novel schemes for universal logic that improve resource overheads. Central to our framework is the description of logical gates holistically in a way which treats space and time on a similar footing. Focusing on schemes based on surface codes, we introduce explicit, but platform-independent representations of topological logic gates -- called logical blocks -- and generate new, overhead-efficient methods for universal quantum computation. As a specific example, we propose fault-tolerant schemes based on surface codes concatenated with more general low-density parity check (LDPC) codes. The logical blocks framework enables a convenient mapping from an abstract description of the logical gate to a precise set of physical instructions for both circuit-based and fusion-based quantum computation (FBQC). Using this, we numerically simulate a surface-code-based universal gate set implemented with FBQC, and verify that their thresholds are consistent with the bulk memory threshold. We find that boundaries, defects, and twists can significantly impact the logical error rate scaling, with periodic boundary conditions potentially halving the resource requirements. Motivated by the favorable logical error rates for boundaryless computation, we introduce a novel computational scheme based on the teleportation of twists that may offer further resource reductions.