Logical gates constitute the building blocks of fault-tolerant quantum computation. While quantum errorcorrected 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 (i) platformindependent logical gate definitions, (ii) flexible and scalable tools for numerical analysis, and (iii) exploration of novel schemes for universal logic that improve resource overheads. We first introduce the theory of faulttolerant logical channels for describing logical gates holistically in space-time. Focusing on channels 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, suggesting an alternative path toward LDPC-based quantum computation. The logical blocks framework enables a convenient software-based mapping from an abstract description of the logical gate to a precise set of physical instructions for executing 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 the threshold for fault-tolerant gates is consistent with the bulk threshold for memory. We find, however, that boundaries, defects, and twists can significantly impact the logical error rate scaling, with periodic boundary conditions potentially halving the memory resource requirements. Motivated by the favorable logical error rate suppression for boundaryless computation, we introduce a novel computational scheme based on the teleportation of twists that may offer further resource reductions.