Neutral atom arrays have recently emerged as a promising platform for fault-tolerant quantum computing.Based on these advances, including dynamically-reconfigurable connectivity and fast transversal operations, we present a low-overhead architecture that supports the layout and resource estimation of large-scale fault-tolerant quantum algorithms.Utilizing recent advances in fault tolerance with transversal gate operations, this architecture achieves a run time speed-up on the order of the code distance 𝑑, which we find directly translates to run time improvements of large-scale quantum algorithms.Our architecture consists of functional building blocks of key algorithmic subroutines, including magic state factories, quantum arithmetic units, and quantum look-up tables.These building blocks are implemented using efficient transversal operations, and we design space-time efficient versions of them that minimize interaction We acknowledge helpful discussions with M. Beverland, A.